A telomere-to-telomere genome assembly of the protandrous hermaphrodite blackhead seabream, Acanthopagrus schlegelii. Sci Data 12:350, 2025. Pubmed reference: 40016269. DOI: 10.1038/s41597-025-04602-y.

2023

Luo, X., Zhang, L., Chen, S. :

Microsatellite genome-wide database development for the commercial blackhead seabream (Acanthopagrus schlegelii). Genes (Basel) 14:620, 2023. Pubmed reference: 36980892. DOI: 10.3390/genes14030620.

Acestrorhynchus altus :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Unraveling the genomic features, phylogeny and genetic basis of tooth ontogenesis in characiformes through analysis of four genomes. DNA Res 30:dsad022, 2023. Pubmed reference: 37788574. DOI: 10.1093/dnares/dsad022.

Acinonyx jubatus (cheetah) :

2023

Winter, S., Meißner, R., Greve, C., Ben Hamadou, A., Horin, P., Prost, S., Burger, P.A. :

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus). J Hered 114:271-278, 2023. Pubmed reference: 36869783. DOI: 10.1093/jhered/esad015.

Acomys cahirinus (Egyptian spiny mouse) :

2023

Nguyen, E.D., Fard, V.N., Kim, B.Y., Collins, S., Galey, M., Nelson, B.R., Wakenight, P., Gable, S.M., McKenna, A., Bammler, T.K., MacDonald, J., Okamura, D.M., Shendure, J., Beier, D.R., Ramirez, J.M., Majesky, M.W., Millen, K.J., Tollis, M., Miller, D.E. :

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). bioRxiv , 2023. Pubmed reference: 37066261. DOI: 10.1101/2023.04.03.535372.

GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda) 13:jkad177, 2023. Pubmed reference: 37552705. DOI: 10.1093/g3journal/jkad177.

Acridotheres tristis (common myna) :

2024

Stuart, K.C., Johnson, R.N., Major, R., Atsawawaranunt, K., Ewart, K.M., Rollins, L.A., Santure, A.W., Whibley, A. :

The genome of a globally invasive passerine, the common myna, Acridotheres tristis. DNA Res 31:dsae005, 2024. Pubmed reference: 38366840. DOI: 10.1093/dnares/dsae005.

Acrossocheilus fasciatus :

2024

Zheng, J., Jiang, J., Rui, Q., Li, F., Liu, S., Cheng, S., Chi, M., Jiang, W. :

Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology. Sci Data 11:166, 2024. Pubmed reference: 38310107. DOI: 10.1038/s41597-024-02999-6.

Yuan, Y., Zhong, T., Wang, Y., Yang, J., Gui, L., Shen, Y., Zhou, J., Chung-Davidson, Y.W., Li, W., Xu, J., Li, J., Li, M., Ren, J. :

Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus. Sci Data 11:653, 2024. Pubmed reference: 38906919. DOI: 10.1038/s41597-024-03504-9.

Actinemys marmorata (Pacific pond turtle) :

2022

Todd, B.D., Jenkinson, T.S., Escalona, M., Beraut, E., Nguyen, O., Sahasrabudhe, R., Scott, P.A., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the northwestern pond turtle, Actinemys marmorata. J Hered 113:624-631, 2022. Pubmed reference: 35665811. DOI: 10.1093/jhered/esac021.

Actinopterygii (ray-finned fishes) :

1991

Klinkhardt, M.B. :

A brief comparison of methods for preparing fish chromosomes: an overview. Cytobios 67:193-208, 1991. Pubmed reference: 1724748.

Lakra, W.S., Rishi, K.K. :

Chromosomes of Indian Fishes - An Annotated List. Indian Journal of Animal Sciences 61:342-349, 1991.

Li, Y.C., Gold, J.R. :

Standard and NOR-Stained Karyotypes of 3 Species of North American Cyprinid Fishes. Texas Journal of Science 43:207-211, 1991.

1990

Gold, J.R., Li, Y.C., Shipley, N.S., Powers, P.K. :

Improved Methods for Working with Fish Chromosomes with a Review of Metaphase Chromosome Banding. Journal of Fish Biology 37:563-575, 1990.

1988

Medrano, L., Bernardi, G., Couturier, J., Dutrillaux, B. :

Chromosome banding and genome compartmentalization in fishes. Chromosoma 96:178-183, 1988.

1987

Mayr, B., Kalat, M., Rab, P., Lambrou, M. :

Band karyotypes and specific types of heterochromatins in several species of Eurpoean percid fishes (Percidea, Pisces). Genetica 75:199-205, 1987.

Addax nasomaculatus :

2025

Zhou, J., Zhou, X.F., Yue, H.S., Chen, W., Li, B., Zhou, B.T., Li, Z.H., Du, Z.C., Mao, Y.F., Wang, W., Wu, D.D., Han, G., Wang, B., Chen, L. :

Genomic insights into the convergent evolution of desert adaptation in camels and antelopes. Zool Res 46:2095-8137(2025)04-0939-14:939-952, 2025. Pubmed reference: 40709535. DOI: 10.24272/j.issn.2095-8137.2024.440.

1996

Claro, F., Hayes, H., Cribiu, E.P. :

The karyotype of the addax and its comparison with karyotypes of other species of Hippotraginae antelopes. Hereditas 124:223-7, 1996. Pubmed reference: 8931355. DOI: 10.1111/j.1601-5223.1996.00223.x.

Agapornis :

2025

Dueker, S., Martin, R., Hains, T., Pirro, S., Willows-Munro, S. :

Full genomes of all nine currently recognized lovebird species (genus Agapornis) sampled from wild populations. Sci Data 12:1057, 2025. Pubmed reference: 40544193. DOI: 10.1038/s41597-025-05316-x.

Agapornis roseicollis (peach-faced lovebird) :

2018

van der Zwan, H., van der Westhuizen, F., Visser, C., van der Sluis, R. :

Draft de novo genome sequence of Agapornis roseicollis for application in avian breeding. Anim Biotechnol 29:241-246, 2018. Pubmed reference: 29035135. DOI: 10.1080/10495398.2017.1367692.

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Agelaius tricolor (tricolored blackbird) :

2023

Ballare, K.M., Escalona, M., Barr, K., Seligmann, W., Sacco, S., Sahasrabudhe, R.M., Nguyen, O., Wyckoff, C., Smith, T.B., Shapiro, B. :

A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor. J Hered 114:44-51, 2023. Pubmed reference: 36099176. DOI: 10.1093/jhered/esac053.

Ahaetulla prasina (Asian vine snakes) :

2023

Tang, C.Y., Zhang, X., Xu, X., Sun, S., Peng, C., Song, M.H., Yan, C., Sun, H., Liu, M., Xie, L., Luo, S.J., Li, J.T. :

Genetic mapping and molecular mechanism behind color variation in the Asian vine snake. Genome Biol 24:46, 2023. Pubmed reference: 36895044. DOI: 10.1186/s13059-023-02887-z.

Ailuropoda melanoleuca (giant panda) :

2024

Guan, D., Sun, S., Song, L., Zhao, P., Nie, Y., Huang, X., Zhou, W., Yan, L., Lei, Y., Hu, Y., Wei, F. :

Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown-and-white coat color in giant pandas. Proc Natl Acad Sci U S A 121:e2317430121, 2024. Pubmed reference: 38437540. DOI: 10.1073/pnas.2317430121.

Lan, T., Yang, S., Li, H., Zhang, Y., Li, R., Sahu, S.K., Deng, W., Liu, B., Shi, M., Wang, S., Du, H., Huang, X., Lu, H., Liu, S., Deng, T., Chen, J., Wang, Q., Han, L., Zhou, Y., Li, Q., Li, D., Kristiansen, K., Wan, Q.H., Liu, H., Fang, S.G. :

Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 121:e2406343121, 2024. Pubmed reference: 39186654. DOI: 10.1073/pnas.2406343121.

2023

Ma, S., Zhu, Y., Wu, H. :

Development and validation of SNP markers for giant panda using a kompetitive allele specific PCR approach. Anim Genet 54:659-661, 2023. Pubmed reference: 37580020. DOI: 10.1111/age.13350.

Yang, S., Lan, T., Wei, R., Zhang, L., Lin, L., Du, H., Huang, Y., Zhang, G., Huang, S., Shi, M., Wang, C., Wang, Q., Li, R., Han, L., Tang, D., Li, H., Zhang, H., Cui, J., Lu, H., Huang, J., Luo, Y., Li, D., Wan, Q.H., Liu, H., Fang, S.G. :

Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 21:222, 2023. Pubmed reference: 37858133. DOI: 10.1186/s12915-023-01691-2.

Akarotaxis nudiceps :

2023

Bista, I., Wood, J.M.D., Desvignes, T., McCarthy, S.A., Matschiner, M., Ning, Z., Tracey, A., Torrance, J., Sims, Y., Chow, W., Smith, M., Oliver, K., Haggerty, L., Salzburger, W., Postlethwait, J.H., Howe, K., Clark, M.S., William Detrich, H., Christina Cheng, C.H., Miska, E.A., Durbin, R. :

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Akodon simulator (White-throated Akodont) :

1996

Aniskin, V.M., Isaev, S.I., Shchipanov, N.A. :

[Comparative cytogenetics of three species of South American field hamsters of the genus Akodon (Rodentia, Cricetidae)]. Genetika 32:83-92, 1996. Pubmed reference: 8647427.

Akodon toba (Chaco grass mouse) :

1996

Aniskin, V.M., Isaev, S.I., Shchipanov, N.A. :

[Comparative cytogenetics of three species of South American field hamsters of the genus Akodon (Rodentia, Cricetidae)]. Genetika 32:83-92, 1996. Pubmed reference: 8647427.

Albula glossodonta (roundjaw bonefish) :

2022

Pickett, B.D., Talma, S., Glass, J.R., Ence, D., Johnson, T.P., Cowley, P.D., Ridge, P.G., Kauwe, J.S.K. :

Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish. GigaByte 2022:gigabyte44, 2022. Pubmed reference: 36968794. DOI: 10.46471/gigabyte.44.

Alces alces (Eurasian elk) :

1993

Gripenberg, U., Wessman, M. :

Restriction Endonuclease Staining Profiles in the C- Heterochromatin of Cervidae. Hereditas 118:251-257, 1993.

1990

Bianchi, M.S., Bianchi, N.O., Gripenberg, U., Wessman, M., Huuhtanen, S. :

Characterization of the heterochromatin in moose (Alces alces) chromosomes. Genetica 80:1-7, 1990. Pubmed reference: 2157629. DOI: 10.1007/BF00120114.

Alectoris barbara (Barbary partridge) :

2024

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

Highlighting chromosomal rearrangements of five species of Galliformes (Domestic fowl, Common and Japanese quail, Barbary and Chukar partridge) and the Houbara bustard, an endangered Otidiformes: banding cytogenetic is a powerful tool. Comp Cytogenet 18:213-237, 2024. Pubmed reference: 39664601. DOI: 10.3897/compcytogen.18.135056.

Alectoris chukar (chukar partridge) :

2024

Zhou, H., Huang, X., Liu, J., Ding, J., Xu, K., Zhu, W., He, C., Yang, L., Zhu, J., Han, C., Qin, C., Luo, H., Chen, K., Jiang, S., Shi, Y., Zeng, J., Weng, Z., Xu, Y., Wang, Q., Zhong, M., Du, B., Song, S., Meng, H. :

De novo phased genome assembly, annotation and population genotyping of Alectoris chukar. Sci Data 11:162, 2024. Pubmed reference: 38307880. DOI: 10.1038/s41597-024-02991-0.

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

Alectoris magna (Przewalski's partridge) :

2023

Wang, X., Xia, W., Teng, X., Lin, W., Xing, Z., Wang, S., Liu, X., Qu, J., Zhao, W., Wang, L. :

Chromosome-level genome assembly of Przevalski's partridge (Alectoris magna). Sci Data 10:829, 2023. Pubmed reference: 38007538. DOI: 10.1038/s41597-023-02655-5.

Alectoris rufa (red-legged partridge) :

2025

Eleiwa, A., Mestre, P., Usie, A., Vilaprinyo, E., Marin-Sanguino, A., Sorribas, A., Richart, C., Salces-Ortiz, J., Fernández, R., Biarnés, M., Antilles, N., Nadal, J., Alves, R. :

The genome sequence of the red-legged partridge, Alectoris rufa Linnaeus 1758. F1000Res 14:855, 2025. Pubmed reference: 41019348. DOI: 10.12688/f1000research.162894.1.

2024

Eleiwa, A., Nadal, J., Vilaprinyo, E., Marin-Sanguino, A., Sorribas, A., Basallo, O., Lucido, A., Richart, C., Pena, R.N., Ros-Freixedes, R., Usie, A., Alves, R. :

Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge. Sci Rep 14:19531, 2024. Pubmed reference: 39174643. DOI: 10.1038/s41598-024-70018-0.

González-Prendes, R., Pena, R.N., Richart, C., Nadal, J., Ros-Freixedes, R. :

Long-read de novo assembly of the red-legged partridge (Alectoris rufa) genome. Sci Data 11:908, 2024. Pubmed reference: 39191744. DOI: 10.1038/s41597-024-03659-5.

Alisterus scapularis :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Alligator mississippiensis (American alligator) :

2017

Rice, E.S., Kohno, S., John, J.S., Pham, S., Howard, J., Lareau, L.F., O'Connell, B.L., Hickey, G., Armstrong, J., Deran, A., Fiddes, I., Platt, R.N., Gresham, C., McCarthy, F., Kern, C., Haan, D., Phan, T., Schmidt, C., Sanford, J.R., Ray, D.A., Paten, B., Guillette, L.J., Green, R.E. :

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res 27:686-696, 2017. Pubmed reference: 28137821. DOI: 10.1101/gr.213595.116.

2014

Green, R.E., Braun, E.L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M.W., St John, J.A., Capella-Gutiérrez, S., Castoe, T.A., Kern, C., Fujita, M.K., Opazo, J.C., Jurka, J., Kojima, K.K., Caballero, J., Hubley, R.M., Smit, A.F., Platt, R.N., Lavoie, C.A., Ramakodi, M.P., Finger, J.W., Suh, A., Isberg, S.R., Miles, L., Chong, A.Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S.C., Edwards, S.V., Lyons, E., Williams, C., Breen, M., Howard, J.T., Gresham, C.R., Peterson, D.G., Schmitz, J., Pollock, D.D., Haussler, D., Triplett, E.W., Zhang, G., Irie, N., Jarvis, E.D., Brochu, C.A., Schmidt, C.J., McCarthy, F.M., Faircloth, B.C., Hoffmann, F.G., Glenn, T.C., Gabaldón, T., Paten, B., Ray, D.A. :

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

1994

Valleley, E.M., Harrison, C.J., Cook, Y., Ferguson, M.W., Sharpe, P.T. :

The karyotype of Alligator mississippiensis, and chromosomal mapping of the ZFY/X homologue, Zfc. Chromosoma 103:502-7, 1994. Pubmed reference: 7720416. DOI: 10.1007/BF00337388.

Alosa sapidissima (American shad) :

2024

Velotta, J.P., Iqbal, A.R., Glenn, E.S., Franckowiak, R.P., Formenti, G., Mountcastle, J., Balacco, J., Tracey, A., Sims, Y., Howe, K., Fedrigo, O., Jarvis, E.D., Therkildsen, N.O. :

A complete assembly and annotation of the American shad genome yields insights into the origins of diadromy. Genome Biol Evol 17:evae276, 2024. Pubmed reference: 39786563. DOI: 10.1093/gbe/evae276.

Amazona aestiva (blue-fronted amazon) :

2018

Wirthlin, M., Lima, N.C.B., Guedes, R.L.M., Soares, A.E.R., Almeida, L.G.P., Cavaleiro, N.P., Loss de Morais, G., Chaves, A.V., Howard, J.T., Teixeira, M.M., Schneider, P.N., Santos, F.R., Schatz, M.C., Felipe, M.S., Miyaki, C.Y., Aleixo, A., Schneider, M.P.C., Jarvis, E.D., Vasconcelos, A.T.R., Prosdocimi, F., Mello, C.V. :

Parrot genomes and the evolution of heightened longevity and cognition. Curr Biol 28:4001-4008.e7, 2018. Pubmed reference: 30528582. DOI: 10.1016/j.cub.2018.10.050.

Amazona vittata (Puerto Rican parrot) :

2012

Oleksyk, T.K., Pombert, J.F., Siu, D., Mazo-Vargas, A., Ramos, B., Guiblet, W., Afanador, Y., Ruiz-Rodriguez, C.T., Nickerson, M.L., Logue, D.M., Dean, M., Figueroa, L., Valentin, R., Martinez-Cruzado, J.C. :

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. Gigascience 1:14, 2012. Pubmed reference: 23587420. DOI: 10.1186/2047-217X-1-14.

Amblyraja radiata (thorny skate) :

2021

Rhie, A., McCarthy, S.A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B.J., Chaisson, M., Gedman, G.L., Cantin, L.J., Thibaud-Nissen, F., Haggerty, L., Bista, I., Smith, M., Haase, B., Mountcastle, J., Winkler, S., Paez, S., Howard, J., Vernes, S.C., Lama, T.M., Grutzner, F., Warren, W.C., Balakrishnan, C.N., Burt, D., George, J.M., Biegler, M.T., Iorns, D., Digby, A., Eason, D., Robertson, B., Edwards, T., Wilkinson, M., Turner, G., Meyer, A., Kautt, A.F., Franchini, P., Detrich, H.W., Svardal, H., Wagner, M., Naylor, G.J.P., Pippel, M., Malinsky, M., Mooney, M., Simbirsky, M., Hannigan, B.T., Pesout, T., Houck, M., Misuraca, A., Kingan, S.B., Hall, R., Kronenberg, Z., Sović, I., Dunn, C., Ning, Z., Hastie, A., Lee, J., Selvaraj, S., Green, R.E., Putnam, N.H., Gut, I., Ghurye, J., Garrison, E., Sims, Y., Collins, J., Pelan, S., Torrance, J., Tracey, A., Wood, J., Dagnew, R.E., Guan, D., London, S.E., Clayton, D.F., Mello, C.V., Friedrich, S.R., Lovell, P.V., Osipova, E., Al-Ajli, F.O., Secomandi, S., Kim, H., Theofanopoulou, C., Hiller, M., Zhou, Y., Harris, R.S., Makova, K.D., Medvedev, P., Hoffman, J., Masterson, P., Clark, K., Martin, F., Howe, K., Flicek, P., Walenz, B.P., Kwak, W., Clawson, H., Diekhans, M., Nassar, L., Paten, B., Kraus, R.H.S., Crawford, A.J., Gilbert, M.T.P., Zhang, G., Venkatesh, B., Murphy, R.W., Koepfli, K.P., Shapiro, B., Johnson, W.E., Di Palma, F., Marques-Bonet, T., Teeling, E.C., Warnow, T., Graves, J.M., Ryder, O.A., Haussler, D., O'Brien, S.J., Korlach, J., Lewin, H.A., Howe, K., Myers, E.W., Durbin, R., Phillippy, A.M., Jarvis, E.D. :

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Amia calva (bowfin) :

2021

Thompson, A.W., Hawkins, M.B., Parey, E., Wcisel, D.J., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O.E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B.L., Childs, K.L., Fontenot, Q., Ferrara, A., David, S.R., McCune, A.R., Dornburg, A., Yoder, J.A., Guiguen, Y., Roest Crollius, H., Berthelot, C., Harris, M.P., Braasch, I. :

The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 53:1373-84, 2021. Pubmed reference: 34462605. DOI: 10.1038/s41588-021-00914-y.

Amphibia (amphibians) :

2024

Pyron, R.A., Pirro, S., Hains, T., Colston, T.J., Myers, E.A., O'Connell, K.A., Beamer, D.A. :

The draft genome sequences of 50 salamander species (Caudata, Amphibia). Biodivers Genomes 2024, 2024. Pubmed reference: 38725637. DOI: 10.56179/001c.116891.

Kosch, T.A., Torres-Sánchez, M., Liedtke, H.C., Summers, K., Yun, M.H., Crawford, A.J., Maddock, S.T., Ahammed, M.S., Araújo, V.L.N., Bertola, L.V., Bucciarelli, G., Carné, A., Carneiro, C.M., Chan, K.O., Chen, Y., Crottini, A., da Silva, J.M., Denton, R.D., Dittrich, C., Themudo, G.E., Farquharson, K.A., Forsdick, N.J., Gilbert, E., Jing, C., Katzenback, B.A., Kotharambath, R., Levis, N.A., Márquez, R., Mazepa, G., Mulder, K.P., Müller, H., O'Connell, M.J., Orozco-terWengel, P., Palomar, G., Petzold, A., Pfennig, D.W., Pfennig, K.S., Reichert, M.S., Robert, J., Scherz, M.D., Siu-Ting, K., Snead, A.A., Stöck, M., Stuckert, A.M.M., Stynoski, J.L., Tarvin, R.D., Valero, K.C.W. :

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. bioRxiv , 2024. Pubmed reference: 39005434. DOI: 10.1101/2024.06.27.601086.

Kosch, T.A., Torres-Sánchez, M., Liedtke, H.C., Summers, K., Yun, M.H., Crawford, A.J., Maddock, S.T., Ahammed, M.S., Araújo, V.L.N., Bertola, L.V., Bucciarelli, G.M., Carné, A., Carneiro, C.M., Chan, K.O., Chen, Y., Crottini, A., da Silva, J.M., Denton, R.D., Dittrich, C., Espregueira Themudo, G., Farquharson, K.A., Forsdick, N.J., Gilbert, E., Che, J., Katzenback, B.A., Kotharambath, R., Levis, N.A., Márquez, R., Mazepa, G., Mulder, K.P., Müller, H., O'Connell, M.J., Orozco-terWengel, P., Palomar, G., Petzold, A., Pfennig, D.W., Pfennig, K.S., Reichert, M.S., Robert, J., Scherz, M.D., Siu-Ting, K., Snead, A.A., Stöck, M., Stuckert, A.M.M., Stynoski, J.L., Tarvin, R.D., Wollenberg Valero, K.C. :

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. BMC Genomics 25:1025, 2024. Pubmed reference: 39487448. DOI: 10.1186/s12864-024-10899-7.

Amphilophus citrinellus (Midas cichlid) :

2022

Kratochwil, C.F., Kautt, A.F., Nater, A., Härer, A., Liang, Y., Henning, F., Meyer, A. :

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes. Nat Commun 13:296, 2022. Pubmed reference: 35027541. DOI: 10.1038/s41467-021-27685-8.

Amphiprion bicinctus (twoband anemonefish) :

2018

Casas, L., Saenz-Agudelo, P., Irigoien, X. :

High-throughput sequencing and linkage mapping of a clownfish genome provide insights on the distribution of molecular players involved in sex change. Sci Rep 8:4073, 2018. Pubmed reference: 29511241. DOI: 10.1038/s41598-018-22282-0.

Amphiprion percula (orange clownfish) :

2019

Lehmann, R., Lightfoot, D.J., Schunter, C., Michell, C.T., Ohyanagi, H., Mineta, K., Foret, S., Berumen, M.L., Miller, D.J., Aranda, M., Gojobori, T., Munday, P.L., Ravasi, T. :

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Mol Ecol Resour 19:570-585, 2019. Pubmed reference: 30203521. DOI: 10.1111/1755-0998.12939.

Anarhynchus dealbatus (White-faced plover) :

2025

Zeng, Y., Tu, J., Ho, H., Niu, X., Lin, H., Cheng, Y., Song, Z., Zheng, C., Liu, Y. :

A Chromosome-level Reference Assembly and Annotation for the White-faced Plover (Charadrius dealbatus) Genome. Genome Biol Evol :evaf219, 2025. Pubmed reference: 41332310. DOI: 10.1093/gbe/evaf219.

Anas acuta (northern pintail) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Nine high-quality Anas genomes provide new insights into Anas evolution and domestication. Cell Rep 44:S2211-1247(25)00248-7:115477, 2025. Pubmed reference: 40173044. DOI: 10.1016/j.celrep.2025.115477.

Anas crecca (Common teal) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Anas platyrhynchos (Mallard) :

2025

Zhao, Q., Yin, Z., Hou, Z. :

Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and "missing" genes in birds. J Anim Sci Biotechnol 16:9, 2025. Pubmed reference: 39828703. DOI: 10.1186/s40104-024-01141-1.

Wang, Z., Guo, Z., Liu, H., Liu, T., Liu, D., Yu, S., Tang, H., Zhang, H., Mou, Q., Zhang, B., Cao, J., Schroyen, M., Hou, S., Zhou, Z. :

A high-quality assembly revealing the PMEL gene for the unique plumage phenotype in Liancheng ducks. Gigascience 14:giae114, 2025. Pubmed reference: 39804725. DOI: 10.1093/gigascience/giae114.

Tao, Q., Huang, A., Qi, J., Yang, Z., Guo, S., Lu, Y., He, X., Han, X., Jiang, S., Xu, M., Bai, Y., Zhang, T., Hu, S., Li, L., Bai, L., Liu, H. :

An mRNA expression atlas for the duck with public RNA-seq datasets. BMC Genomics 26:268, 2025. Pubmed reference: 40102741. DOI: 10.1186/s12864-025-11385-4.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Fang, L., Teng, J., Lin, Q., Bai, Z., Liu, S., Guan, D., Li, B., Gao, Y., Hou, Y., Gong, M., Pan, Z., Yu, Y., Clark, E.L., Smith, J., Rawlik, K., Xiang, R., Chamberlain, A.J., Goddard, M.E., Littlejohn, M., Larson, G., MacHugh, D.E., O'Grady, J.F., Sørensen, P., Sahana, G., Lund, M.S., Jiang, Z., Pan, X., Gong, W., Zhang, H., He, X., Zhang, Y., Gao, N., He, J., Yi, G., Liu, Y., Tang, Z., Zhao, P., Zhou, Y., Fu, L., Wang, X., Hao, D., Liu, L., Chen, S., Young, R.S., Shen, X., Xia, C., Cheng, H., Ma, L., Cole, J.B., Baldwin, R.L., Li, C.J., Van Tassell, C.P., Rosen, B.D., Bhowmik, N., Lunney, J., Liu, W., Guan, L., Zhao, X., Ibeagha-Awemu, E.M., Luo, Y., Lin, L., Canela-Xandri, O., Derks, M.F.L., Crooijmans, R.P.M.A., Gòdia, M., Madsen, O., Groenen, M.A.M., Koltes, J.E., Tuggle, C.K., McCarthy, F.M., Rocha, D., Giuffra, E., Amills, M., Clop, A., Ballester, M., Tosser-Klopp, G., Li, J., Fang, C., Fang, M., Wang, Q., Hou, Z., Wang, Q., Zhao, F., Jiang, L., Zhao, G., Zhou, Z., Zhou, R., Liu, H., Deng, J., Jin, L., Li, M., Mo, D., Liu, X., Chen, Y., Yuan, X., Li, J., Zhao, S., Zhang, Y., Ding, X., Sun, D., Sun, H.Z., Li, C., Wang, Y., Jiang, Y., Wu, D., Wang, W., Fan, X., Zhang, Q., Li, K., Zhang, H., Yang, N., Hu, X., Huang, W., Song, J., Wu, Y., Yang, J., Wu, W., Kasper, C., Liu, X., Yu, X., Cui, L., Zhou, X., Kim, S., Li, W., Im, H.K., Buckler, E.S., Ren, B., Schatz, M.C., Li, J.J., Palmer, A.A., Frantz, L., Zhou, H., Zhang, Z., Liu, G.E. :

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

Li, L., Quan, J., Liu, H., Yu, H., Chen, H., Xia, C., Zhao, S., Gao, C. :

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 25:17, 2024. Pubmed reference: 38166615. DOI: 10.1186/s12864-023-09928-8.

Hu, J., Song, L., Ning, M., Niu, X., Han, M., Gao, C., Feng, X., Cai, H., Li, T., Li, F., Li, H., Gong, D., Song, W., Liu, L., Pu, J., Liu, J., Smith, J., Sun, H., Huang, Y. :

A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 22:31, 2024. Pubmed reference: 38317190. DOI: 10.1186/s12915-024-01817-0.

2023

Yu, S., Liu, Z., Li, M., Zhou, D., Hua, P., Cheng, H., Fan, W., Xu, Y., Liu, D., Liang, S., Zhang, Y., Xie, M., Tang, J., Jiang, Y., Hou, S., Zhou, Z. :

Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection. Gigascience 12:giad016, 2023. Pubmed reference: 36971291. DOI: 10.1093/gigascience/giad016.

Lavretsky, P., Hernández, F., Swale, T., Mohl, J.E. :

Chromosomal-level reference genome of a wild North American mallard (Anas platyrhynchos). G3 (Bethesda) 13:jkad171, 2023. Pubmed reference: 37523777. DOI: 10.1093/g3journal/jkad171.

Gu, H., Wen, J., Zhao, X., Zhang, X., Ren, X., Cheng, H., Qu, L. :

Evolution, inheritance, and strata formation of the W chromosome in duck (Anas platyrhynchos). Genome Biol Evol 15:evad183, 2023. Pubmed reference: 37931036. DOI: 10.1093/gbe/evad183.

2021

Zhu, F., Yin, Z.T., Wang, Z., Smith, J., Zhang, F., Martin, F., Ogeh, D., Hincke, M., Lin, F.B., Burt, D.W., Zhou, Z.K., Hou, S.S., Zhao, Q.S., Li, X.Q., Ding, S.R., Li, G.S., Yang, F.X., Hao, J.P., Zhang, Z., Lu, L.Z., Yang, N., Hou, Z.C. :

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun 12:5932, 2021. Pubmed reference: 34635656. DOI: 10.1038/s41467-021-26272-1.

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

Comparative mapping of the macrochromosomes of eight avian species provides further insight into their phylogenetic relationships and avian karyotype evolution. Cells 10:362, 2021. Pubmed reference: 33572408. DOI: 10.3390/cells10020362.

2013

Huang, Y., Li, Y., Burt, D.W., Chen, H., Zhang, Y., Qian, W., Kim, H., Gan, S., Zhao, Y., Li, J., Yi, K., Feng, H., Zhu, P., Li, B., Liu, Q., Fairley, S., Magor, K.E., Du, Z., Hu, X., Goodman, L., Tafer, H., Vignal, A., Lee, T., Kim, K.W., Sheng, Z., An, Y., Searle, S., Herrero, J., Groenen, M.A., Crooijmans, R.P., Faraut, T., Cai, Q., Webster, R.G., Aldridge, J.R., Warren, W.C., Bartschat, S., Kehr, S., Marz, M., Stadler, P.F., Smith, J., Kraus, R.H., Zhao, Y., Ren, L., Fei, J., Morisson, M., Kaiser, P., Griffin, D.K., Rao, M., Pitel, F., Wang, J., Li, N. :

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 45:776-83, 2013. Pubmed reference: 23749191. DOI: 10.1038/ng.2657.

1997

Denjean, B., Ducos, A., Darre, A., Pinton, A., Seguela, A., Berland, H., Blanc, M.F., Fillon, V., Darre, R. :

Karyotypes of mallard (anas platyrhynchos) and muscovy (cairina moschata) ducks, and of their hybrid [French]. Revue de Medecine Veterinaire 148:695-704, 1997.

Anas platyrhynchos x Cairina moschata (domestic duck x muscovy duck) :

2024

Che, T., Li, J., Li, X., Wang, Z., Zhang, X., Yang, W., Liu, T., Wang, Y., Wang, K., Gao, T., Shen, G., Qiu, W., Li, Z., Zhang, W. :

Haplotype-resolved assembly of the mule duck genome using high-fidelity sequencing technology. PLoS One 19:e0305914, 2024. Pubmed reference: 38950038. DOI: 10.1371/journal.pone.0305914.

1997

Denjean, B., Ducos, A., Darre, A., Pinton, A., Seguela, A., Berland, H., Blanc, M.F., Fillon, V., Darre, R. :

Karyotypes of mallard (anas platyrhynchos) and muscovy (cairina moschata) ducks, and of their hybrid [French]. Revue de Medecine Veterinaire 148:695-704, 1997.

1986

Tesoro, M., Migliore, L., Romboli, I. :

[The karyotype of a duck hybrid: Anas platyrhyhchos X Cairina moschata]. Annali della Facolta di Medicina Veterinaria di Pisa 39:153-158, 1986.

Anas zonorhyncha (eastern spot-billed duck) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Anatidae (waterfowl) :

2024

Griffith, E., Pirro, S. :

The complete genome sequences of 29 species of ducks (Anatidae, Anseriformes). Biodivers Genomes 2024, 2024. Pubmed reference: 39118967. DOI: 10.56179/001c.122134.

Andrias davidianus (Chinese giant salamander) :

2021

Hu, Q., Liu, Y., Liao, X., Tian, H., Ji, X., Zhu, J., Xiao, H. :

A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander. BMC Genomics 22:230, 2021. Pubmed reference: 33794798. DOI: 10.1186/s12864-021-07550-0.

Anguilla bicolor (Indonesian shortfin eel) :

2024

Choi, H., Nam, J., Yang, S., Eyun, S.I. :

Highly contiguous genome assembly and gene annotation of the short-finned eel (Anguilla bicolor pacifica). Sci Data 11:952, 2024. Pubmed reference: 39214993. DOI: 10.1038/s41597-024-03817-9.

Anisarchus medius (stout eelblenny) :

2025

Liu, R., Meng, Z., Mu, Y., Zhang, R., Ma, H., Hu, J., Wang, Y., Shi, Y., Li, Y., Wang, C., Zhang, W., Lin, L., Zheng, P., Chen, X. :

Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius. Sci Data 12:68, 2025. Pubmed reference: 39809797. DOI: 10.1038/s41597-025-04419-9.

Anolis apletophallus (slender anole) :

2023

Pirani, R.M., Arias, C.F., Charles, K., Chung, A.K., Curlis, J.D., Nicholson, D.J., Vargas, M., Cox, C.L., McMillan, W.O., Logan, M.L. :

A high-quality genome for the slender anole (Anolis apletophallus), an emerging model for field-studies of tropical ecology and evolution. G3 (Bethesda) 14:jkad248, 2023. Pubmed reference: 37875105. DOI: 10.1093/g3journal/jkad248.

Anomalopteryx didiformis (little bush moa) :

2024

Edwards, S.V., Cloutier, A., Cockburn, G., Driver, R., Grayson, P., Katoh, K., Baldwin, M.W., Sackton, T.B., Baker, A.J. :

A nuclear genome assembly of an extinct flightless bird, the little bush moa. Sci Adv 10:eadj6823, 2024. Pubmed reference: 38781323. DOI: 10.1126/sciadv.adj6823.

Anoplopoma fimbria (sablefish) :

2023

Flores, A.M., Christensen, K.A., Campbell, B., Koop, B.F., Taylor, J.S. :

Sablefish (Anoplopoma fimbria) chromosome-level genome assembly. G3 (Bethesda) 13:jkad089, 2023. Pubmed reference: 37097026. DOI: 10.1093/g3journal/jkad089.

Anser anser (domestic goose) :

2025

Huang, M., Sun, J., Wang, J., Ye, X., Chen, Z., Zhao, X., Zhang, K., Ma, L., Xue, J., Luo, Y., Wu, X., Wang, H., Wang, C., Liu, Z., Xie, Y., Chen, Y., Wang, Q., Wang, Y., Gao, G. :

Goose multi-omics database: A comprehensive multi-omics database for goose genomics. Poult Sci 104:S0032-5791(25)00079-3:104842, 2025. Pubmed reference: 39874782. DOI: 10.1016/j.psj.2025.104842.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

Zhou, Y., Mabrouk, I., Ma, J., Liu, Q., Song, Y., Xue, G., Li, X., Wang, S., Liu, C., Hu, J., Sun, Y. :

Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development. Poult Sci 103:S0032-5791(24)00512-1:103933, 2024. Pubmed reference: 38943801. DOI: 10.1016/j.psj.2024.103933.

2023

Gao, G., Zhang, H., Ni, J., Zhao, X., Zhang, K., Wang, J., Kong, X., Wang, Q. :

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis. J Anim Sci Biotechnol 14:150, 2023. Pubmed reference: 38001525. DOI: 10.1186/s40104-023-00944-y.

1988

Silversides, F.G., Crawford, R.D., Wang, H.C. :

The cytogenetics of domestic geese. J Hered 79:6-8, 1988. Pubmed reference: 3367038. DOI: 10.1093/oxfordjournals.jhered.a110449.

Anser cygnoides (swan goose) :

2025

Zhang, L., Huang, Z., Luo, M., Wu, Z., Zhang, X., Chen, J., Lin, Z., Tian, Y., Huang, Y., Li, X. :

Whole-genome sequencing reveals copy number variations and their associations with body weight and size traits at slaughter in Lion-head geese. Poult Sci 104:S0032-5791(25)00129-4:104892, 2025. Pubmed reference: 39965273. DOI: 10.1016/j.psj.2025.104892.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

2024

Zhao, H., Zhou, H., Sun, G., Dong, B., Zhu, W., Mu, X., Li, X., Wang, J., Zhao, M., Yang, W., Zhang, G., Ji, R., Geng, T., Gong, D., Meng, H., Wang, J. :

Telomere-to-telomere genome assembly of the goose Anser cygnoides. Sci Data 11:741, 2024. Pubmed reference: 38972874. DOI: 10.1038/s41597-024-03567-8.

2023

Ni, H., Zhang, Y., Yang, Y., Yin, Y., Xie, H., Zheng, J., Dong, L., Diao, J., Wei, M., Lv, Z., Yan, S., Li, Y., Sun, H., Sun, X. :

Whole genome sequencing of a wild swan goose population. Front Genet 14:1038606, 2023. Pubmed reference: 36911404. DOI: 10.3389/fgene.2023.1038606.

2022

Zhang, Y., Ni, H., Xie, H., Yin, Y., Zheng, J., Dong, L., Diao, J., Yan, S., Yang, Y., Sun, H., Sun, X. :

De novo assembly of a wild swan goose (Anser cygnoides) genome. Anim Genet 53:878-880, 2022. Pubmed reference: 36086875. DOI: 10.1111/age.13262.

2015

Lu, L., Chen, Y., Wang, Z., Li, X., Chen, W., Tao, Z., Shen, J., Tian, Y., Wang, D., Li, G., Chen, L., Chen, F., Fang, D., Yu, L., Sun, Y., Ma, Y., Li, J., Wang, J. :

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. Genome Biol 16:89, 2015. Pubmed reference: 25943208. DOI: 10.1186/s13059-015-0652-y.

1988

Silversides, F.G., Crawford, R.D., Wang, H.C. :

The cytogenetics of domestic geese. J Hered 79:6-8, 1988. Pubmed reference: 3367038. DOI: 10.1093/oxfordjournals.jhered.a110449.

Antennarius striatus (striated frogfish) :

2024

Hu, M., Fan, D., Hao, J., Zhang, F., Xu, W., Zhu, C., Wang, K., Song, X., Li, L. :

A chromosome-level genome of the striated frogfish (Antennarius striatus). Sci Data 11:654, 2024. Pubmed reference: 38906880. DOI: 10.1038/s41597-024-03514-7.

Antidorcas marsupialis (springbok) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Antilope cervicapra (blackbuck) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Apareiodon sp. 'Rio Verde' :

2024

Wolf, I.R., Schemberger, M.O., Azambuja, M., Oliveira, F.S., Nogaroto, V., Valente, G.T., Martins, C., Vicari, M.R. :

The long-read assembly of Apareiodon sp., a neotropical fish with a ZZ/ZW sex chromosome system. Genet Mol Biol 47:e20240098, 2024. Pubmed reference: 39392722. DOI: 10.1590/1678-4685-GMB-2024-0098.

Aphelocoma californica (Western scrub-jay) :

2023

DeRaad, D.A., Escalona, M., Benham, P., Marimuthu, M.P.A., Sahasrabudhe, R.M., Nguyen, O., Chumchim, N., Beraut, E., Fairbairn, C.W., Seligmann, W., Bowie, R.C.K., Cicero, C., McCormack, J.E., Wayne, R.K. :

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. J Hered 114:669-680, 2023. Pubmed reference: 37589384. DOI: 10.1093/jhered/esad047.

Aphelocoma coerulescens (scrub jay) :

2024

Romero, F.G., Beaudry, F.E.G., Hovmand Warner, E., Nguyen, T.N., Fitzpatrick, J.W., Chen, N. :

A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens). G3 (Bethesda) 14:jkae232, 2024. Pubmed reference: 39328063. DOI: 10.1093/g3journal/jkae232.

Apis mellifera (honey bee) :

2023

Parejo, M., Talenti, A., Richardson, M., Vignal, A., Barnett, M., Wragg, D. :

AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap. Sci Data 10:198, 2023. Pubmed reference: 37037860. DOI: 10.1038/s41597-023-02097-z.

Duhan, N., Kaur, S., Kaundal, R. :

ranchSATdb: A genome-wide simple sequence repeat (SSR) markers database of livestock species for mutant germplasm characterization and improving farm animal health. Genes (Basel) 14:1481, 2023. Pubmed reference: 37510385. DOI: 10.3390/genes14071481.

Apricaphanius iberus (Spanish toothcarp) :

2025

López-Solano, A., Doadrio, I., Nester, T.L., Perea, S. :

De novo genome hybrid assembly and annotation of the endangered and euryhaline fish Aphanius iberus (Valenciennes, 1846) with identification of genes potentially involved in salinity adaptation. BMC Genomics 26:136, 2025. Pubmed reference: 39939939. DOI: 10.1186/s12864-025-11327-0.

Aquarana catesbeiana (bullfrog) :

2025

Zhang, K., Zhang, Y., Tian, Y., Xu, B., Jiang, X., Qin, Z., Liu, C., Lin, L. :

A Chromosome-level genome assembly of the American bullfrog (Aquarana catesbeiana). Sci Data 12:413, 2025. Pubmed reference: 40064910. DOI: 10.1038/s41597-025-04697-3.

Ara macao (scarlet macaw) :

2013

Seabury, C.M., Dowd, S.E., Seabury, P.M., Raudsepp, T., Brightsmith, D.J., Liboriussen, P., Halley, Y., Fisher, C.A., Owens, E., Viswanathan, G., Tizard, I.R. :

A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 8:e62415, 2013. Pubmed reference: 23667475. DOI: 10.1371/journal.pone.0062415.

Aratinga solstitialis (sun parakeet) :

2020

Gelabert, P., Sandoval-Velasco, M., Serres, A., de Manuel, M., Renom, P., Margaryan, A., Stiller, J., de-Dios, T., Fang, Q., Feng, S., Mañosa, S., Pacheco, G., Ferrando-Bernal, M., Shi, G., Hao, F., Chen, X., Petersen, B., Olsen, R.A., Navarro, A., Deng, Y., Dalén, L., Marquès-Bonet, T., Zhang, G., Antunes, A., Gilbert, M.T.P., Lalueza-Fox, C. :

Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Curr Biol 30:108-114.e5, 2020. Pubmed reference: 31839456. DOI: 10.1016/j.cub.2019.10.066.

Archilochus colubris :

2023

Gershman, A., Hauck, Q., Dick, M., Jamison, J.M., Tassia, M., Agirrezabala, X., Muhammad, S., Ali, R., Workman, R.E., Valle, M., Wong, G.W., Welch, K.C., Timp, W. :

Genomic insights into metabolic flux in hummingbirds. Genome Res 33:703-714, 2023. Pubmed reference: 37156619. DOI: 10.1101/gr.276779.122.

Archocentrus centrarchus (flier cichlid) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Arctocephalus gazella (antarctic fur seal) :

2024

Hench, K., Vendrami, D.L.J., Forcada, J., Hoffman, J.I. :

Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness. G3 (Bethesda) 14:jkae179, 2024. Pubmed reference: 39082761. DOI: 10.1093/g3journal/jkae179.

Argyrosomus japonicus (mulloway) :

2024

Jackson, T.K., Rhode, C. :

Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits. J Fish Biol 105:841-857, 2024. Pubmed reference: 38885946. DOI: 10.1111/jfb.15844.

Ariidae (sea catfishes) :

2024

Sandoval, M.M.R., Pirro, S., Betancur, R. :

The draft genome sequences of 63 species of catfish (Ariidae, Siluriformes). Biodivers Genomes 2024, 2024. Pubmed reference: 38817348. DOI: 10.56179/001c.117717.

Arizona elegans occidentalis :

2022

Wood, D.A., Richmond, J.Q., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Westphal, M., Fisher, R.N., Vandergast, A.G., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California species of special concern. J Hered 113:632-640, 2022. Pubmed reference: 35939354. DOI: 10.1093/jhered/esac040.

Asaccus caudivolvulus :

2024

Burriel-Carranza, B., Mochales-Riaño, G., Talavera, A., Els, J., Estarellas, M., Al Saadi, S., Urriago Suarez, J.D., Olsson, P.O., Matschiner, M., Carranza, S. :

Clinging on the brink: Whole genomes reveal human-induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf-toed Gecko (Asaccus caudivolvulus). Mol Ecol 33:e17451, 2024. Pubmed reference: 38970417. DOI: 10.1111/mec.17451.

Aselliscus stoliczkanus (Stoliczka's Asian trident bat) :

2023

Lan, L., Zhang, X., Yang, S., Li, L., Mao, X. :

Chromosome-level genome assembly of the Stoliczka's Asian trident bat (Aselliscus stoliczkanus). Sci Data 10:902, 2023. Pubmed reference: 38102156. DOI: 10.1038/s41597-023-02838-0.

Asio madagascariensis :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Astatotilapia calliptera (eastern happy) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Astyanax mexicanus (Mexican tetra) :

2024

Warren, W.C., Rice, E.S., X, M., Roback, E., Keene, A., Martin, F., Ogeh, D., Haggerty, L., Carroll, R.A., McGaugh, S., Rohner, N. :

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. G3 (Bethesda) 14:jkae103, 2024. Pubmed reference: 38771704. DOI: 10.1093/g3journal/jkae103.

2023

Warren, W.C., Rice, E.S., Maggs, X., Roback, E., Keene, A., Martin, F., Ogeh, D., Haggerty, L., Carroll, R.A., McGaugh, S., Rohner, N. :

Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. bioRxiv , 2023. Pubmed reference: 38014157. DOI: 10.1101/2023.11.16.567450.

2014

McGaugh, S.E., Gross, J.B., Aken, B., Blin, M., Borowsky, R., Chalopin, D., Hinaux, H., Jeffery, W.R., Keene, A., Ma, L., Minx, P., Murphy, D., O'Quin, K.E., Rétaux, S., Rohner, N., Searle, S.M., Stahl, B.A., Tabin, C., Volff, J.N., Yoshizawa, M., Warren, W.C. :

The cavefish genome reveals candidate genes for eye loss. Nat Commun 5:5307, 2014. Pubmed reference: 25329095. DOI: 10.1038/ncomms6307.

2002

Borowsky, R., Wilkens, H. :

Mapping a cave fish genome: polygenic systems and regressive evolution. J Hered 93:19-21, 2002. Pubmed reference: 12011170. DOI: 10.1093/jhered/93.1.19.

Atelerix albiventris (middle-African hedgehog) :

2024

Jiang, L., Xu, J., Zhu, M., Lv, Z., Ning, Z., Yang, F. :

A haplotype-resolved genome reveals the genetic basis of spine formation in Atelerix albiventris. J Genet Genomics 51:1529-1532, 2024. Pubmed reference: 38950858. DOI: 10.1016/j.jgg.2024.06.012.

Ateles fusciceps (brown-headed spider monkey) :

2024

Pozo, G., Albuja-Quintana, M., Larreátegui, L., Gutiérrez, B., Fuentes, N., Alfonso-Cortés, F., de Lourdes Torres, M. :

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (Bethesda) 14:jkae014, 2024. Pubmed reference: 38244218. DOI: 10.1093/g3journal/jkae014.

Ateles paniscus (black spider monkey) :

2025

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Monfort Anez, G., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

Atelopus laetissimus (Santa Marta harlequin toad) :

2025

Araújo, V.L.N., Grau, J.H., Rueda-Solano, L.A., Barros-Castañeda, J.D., Flechas, S.V., Crawford, A.J. :

Genome assembly of the endangered Santa Marta Harlequin Toad, Atelopus laetissimus, endemic to the Sierra Nevada de Santa Marta of Colombia. J Hered 116:673-679, 2025. Pubmed reference: 40369906. DOI: 10.1093/jhered/esaf029.

Atractosteus spatula (alligator gar) :

2024

Wang, Q., Yu, Q., Dong, X., Chen, H., Tian, X., Qi, P., Wu, H., Yuan, Y. :

Chromosome-scale genome assembly and gene annotation of the Alligator Gar (Atractosteus spatula). Sci Data 11:1337, 2024. Pubmed reference: 39695265. DOI: 10.1038/s41597-024-04256-2.

Aythya baeri (Baer's pochard) :

2023

Zhang, L., Gao, X., Xia, T., Yang, X., Sun, G., Zhao, C., Liu, G., Zhang, H. :

Chromosome-level genome assembly of the critically endangered Baer's pochard (Aythya baeri). Sci Data 10:176, 2023. Pubmed reference: 36991020. DOI: 10.1038/s41597-023-02063-9.

Aythya ferina (common pochard) :

2024

Xia, T., Gao, X., Zhang, L., Zhou, S., Zhang, Z., Ding, J., Sun, G., Yang, X., Zhang, H. :

Chromosome-level genome provides insights into evolution and diving adaptability in the vulnerable common pochard (Aythya ferina). BMC Genomics 25:927, 2024. Pubmed reference: 39363174. DOI: 10.1186/s12864-024-10846-6.

Aythya fuligula (tufted duck) :

2021

Mueller, R.C., Ellström, P., Howe, K., Uliano-Silva, M., Kuo, R.I., Miedzinska, K., Warr, A., Fedrigo, O., Haase, B., Mountcastle, J., Chow, W., Torrance, J., Wood, J.M.D., Järhult, J.D., Naguib, M.M., Olsen, B., Jarvis, E.D., Smith, J., Eöry, L., Kraus, R.H.S. :

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience 10:giab081, 2021. Pubmed reference: 34927191. DOI: 10.1093/gigascience/giab081.

Aythya marila (greater scaup) :

2023

Zhou, S., Xia, T., Gao, X., Lyu, T., Wang, L., Wang, X., Shi, L., Dong, Y., Zhang, H. :

A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila). Sci Data 10:254, 2023. Pubmed reference: 37142629. DOI: 10.1038/s41597-023-02142-x.

Aythya nyroca :

2025

Ding, J., Xia, T., Li, S., Gao, X., Yao, Z., Zhou, S., Zhang, L., Zhang, Z., Chen, S., Han, M., Zhang, H. :

Chromosome-level assembly of the genome of the Aythya nyroca provides insights into diving adaptations. Genomics 117:111103, 2025. Pubmed reference: 40945622. DOI: 10.1016/j.ygeno.2025.111103.

Azemiops feae :

2025

[No authors listed] :

Correction to: De novo genome assembly highlights the role of lineage-specific gene duplications in the evolution of venom in Fea's viper (Azemiops feae). Genome Biol Evol 17:evaf033, 2025. Pubmed reference: 40083206. DOI: 10.1093/gbe/evaf033.

Bahaba taipingensis (Chinese bahaba) :

2024

Cui, R., Wu, J., Yan, K., Luo, S., Hu, Y., Feng, W., Lu, B., Wang, J. :

Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae). Mol Ecol 33:e17250, 2024. Pubmed reference: 38179694. DOI: 10.1111/mec.17250.

Balaenoptera edeni (pygmy Bryde's whale) :

2025

Lin, Y.T., Hui, F., Han, W., Li, Y.X., Heung, B.Y.W., How, C.M., Wang, S., Qiu, J.W. :

Chromosome-level genome assembly of Eden's whale clarifies the taxonomy and speciation of Bryde's whale complex. Mol Biol Evol 42:msaf234, 2025. Pubmed reference: 40973465. DOI: 10.1093/molbev/msaf234.

Balaenoptera musculus (Blue whale) :

2024

Bukhman, Y.V., Morin, P.A., Meyer, S., Chu, L.F., Jacobsen, J.K., Antosiewicz-Bourget, J., Mamott, D., Gonzales, M., Argus, C., Bolin, J., Berres, M.E., Fedrigo, O., Steill, J., Swanson, S.A., Jiang, P., Rhie, A., Formenti, G., Phillippy, A.M., Harris, R.S., Wood, J.M.D., Howe, K., Kirilenko, B.M., Munegowda, C., Hiller, M., Jain, A., Kihara, D., Johnston, J.S., Ionkov, A., Raja, K., Toh, H., Lang, A., Wolf, M., Jarvis, E.D., Thomson, J.A., Chaisson, M.J.P., Stewart, R. :

A high-quality blue whale genome, segmental duplications, and historical demography. Mol Biol Evol 41:msae036, 2024. Pubmed reference: 38376487. DOI: 10.1093/molbev/msae036.

Bangana tungting (Dongting carp) :

2025

Xie, X., Zou, L., Chen, F., Zhang, Z., Han, L., Xiang, X., Li, S., Xie, Z., Liang, Z. :

Chromosome-level genome assembly of Decorus tungting, an endemic cyprinid from China. Sci Data 12:1739, 2025. Pubmed reference: 41188269. DOI: 10.1038/s41597-025-06017-1.

Barbatula barbatula (stone loach) :

2025

Laczkó, L., Nagy, N.A., Nagy, Á., Maroda, Á., Sály, P. :

An updated reference genome of Barbatula barbatula (Linnaeus, 1758). Sci Data 12:137, 2025. Pubmed reference: 39843539. DOI: 10.1038/s41597-025-04469-z.

Barbodes semifasciolatus (Chinese barb) :

2025

Chen, W., Li, C., Yang, R., Li, Y., Wu, B., Li, J. :

Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus). Sci Data 12:902, 2025. Pubmed reference: 40442123. DOI: 10.1038/s41597-025-05178-3.

Barbodes wynaadensis :

2025

Shen, Q., Wu, J., Yang, C., Sheng, Q., Xu, M., Yi, S., Song, J. :

Chromosome-level assembly and annotation of the yellow-shelled fish (Barbodes Wynaadensis). Sci Data 12:1196, 2025. Pubmed reference: 40646004. DOI: 10.1038/s41597-025-05547-y.

Bathydraco marri (deepwater dragon) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Beatragus hunteri :

1996

Kumamoto, A.T., Charter, S.J., Houck, M.L., Frahm, M. :

Chromosomes of Damaliscus (Artiodactyla, Bovidae): simple and complex centric fusion rearrangements. Chromosome Res 4:614-21, 1996. Pubmed reference: 9024978. DOI: 10.1007/BF02261724.

Bettongia gaimardi (Tasmanian bettong) :

2024

Silver, L.W., Edwards, R.J., Neaves, L., Manning, A., Hogg, C.J., Banks, S. :

A reference genome for the eastern bettong (Bettongia gaimardi). F1000Res 13:1544, 2024. Pubmed reference: 39816984. DOI: 10.12688/f1000research.157851.1.

Bison bison (American bison) :

2024

Stroupe, S., Derr, J.N. :

Development and evaluation of a novel single nucleotide polymorphism panel for North American bison. Evol Appl 17:e13658, 2024. Pubmed reference: 38390379. DOI: 10.1111/eva.13658.

2023

Stroupe, S., Martone, C., McCann, B., Juras, R., Kjöllerström, H.J., Raudsepp, T., Beard, D., Davis, B.W., Derr, J.N. :

Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation. G3 (Bethesda) 13:jkad156, 2023. Pubmed reference: 37481261. DOI: 10.1093/g3journal/jkad156.

2021

Dobson, L.K., Zimin, A., Bayles, D., Fritz-Waters, E., Alt, D., Olsen, S., Blanchong, J., Reecy, J., Smith, T.P.L., Derr, J.N. :

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Anim Genet 52:263-274, 2021. Pubmed reference: 33780561. DOI: 10.1111/age.13060.

Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. :

A reference genome assembly of American bison, Bison bison bison. J Hered 112:174-183, 2021. Pubmed reference: 33595645. DOI: 10.1093/jhered/esab003.

1967

Basrur, P.K., Moon, Y.S. :

Chromosomes of cattle, bison, and their hybrid, the cattalo. Am J Vet Res 28:1319-25, 1967. Pubmed reference: 6053538.

Bison bonasus (European bison) :

2024

Wehrenberg, G., Tokarska, M., Cocchiararo, B., Nowak, C. :

A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Sci Rep 14:1875, 2024. Pubmed reference: 38253649. DOI: 10.1038/s41598-024-51495-9.

Bortoluzzi, C., Mapel, X.M., Neuenschwander, S., Janett, F., Pausch, H., Leonard, A.S. :

Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene. Commun Biol 7:1580, 2024. Pubmed reference: 39604663. DOI: 10.1038/s42003-024-07295-y.

Blastocerus dichotomus (marsh deer) :

1995

Duarte, J.M.B., Giannoni, M.L. :

Cytogenetic analysis of the Marsh Deer, Blastocerus dichotomus (Mammalia, Cervidae). Revista Brasileira de Genetica 18:245-248, 1995.

Boaedon fuliginosus (brown house snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Boleophthalmus pectinirostris (great blue-spotted mudskipper) :

2024

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation. J Adv Res 58:S2090-1232(23)00143-1:93-104, 2024. Pubmed reference: 37220853. DOI: 10.1016/j.jare.2023.05.005.

Bombyx mori (domestic silkworm) :

2023

Waizumi, R., Tsubota, T., Jouraku, A., Kuwazaki, S., Yokoi, K., Iizuka, T., Yamamoto, K., Sezutsu, H. :

Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01. G3 (Bethesda) 13:jkad044, 2023. Pubmed reference: 36814357. DOI: 10.1093/g3journal/jkad044.

Bos frontalis (gayal) :

2025

Gao, Z., Wang, B., Lu, Y., Chong, Y., Li, M., Hong, J., Wu, J., Xi, D., Deng, W. :

De novo transcriptome assembly and annotation of the semi-wild Gayal (Bos frontalis). Sci Data 12:589, 2025. Pubmed reference: 40199884. DOI: 10.1038/s41597-025-04927-8.

1995

Gupta, N., Verma, N.D., Gupta, S.C., Kumar, P., Sahai, R. :

Chromosomes of mithun (Gaveaus frontalis). Indian Journal of Animal Sciences 65:688-690, 1995.

1987

Namikawa, T., Amano, T., Okada, I., Hasnath, M.A., Haque, A.K.F., Majid, M.A. :

Karyotypes, blood groups and blood protein polymorphisms in the gayal, gayal-cattle hybrid and native cattle of Bangladesh. Genetic studies on breed differentiation of the native domestic animals in Bangladesh. Faculty of Applied Biological Science, Hiroshima University, Hiroshima :105-115, 1987.

Bos gaurus (gaur) :

2025

Nguyen, T.D.T., Tran, T.B.N., Nguyen, L.T. :

Genome assembly of the Bos gaurus in Vietnam using nanopore sequencing. BMC Genom Data 26:42, 2025. Pubmed reference: 40597655. DOI: 10.1186/s12863-025-01331-4.

2022

Low, W.Y., Rosen, B.D., Ren, Y., Bickhart, D.M., To, T.H., Martin, F.J., Billis, K., Sonstegard, T.S., Sullivan, S.T., Hiendleder, S., Williams, J.L., Heaton, M.P., Smith, T.P.L. :

Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics 23:344, 2022. Pubmed reference: 35508966. DOI: 10.1186/s12864-022-08561-1.

1988

Bongso, T.A., Hilmi, M., Sopian, M., Zulkifli, S. :

Chromosomes of gaur cross domestic cattle hybrids. Res Vet Sci 44:251-4, 1988. Pubmed reference: 3387680.

Bos grunniens (domestic yak) :

2025

Pukhrambam, M., Tribhuvan, K.U., Paul, V., Pandey, A., Dutta, A., Bhadana, V.P., Dabas, S., Ramakrushna, G.I., Raghavendra, K.P., Verma, P., Prasad, Y.G., Mohanty, A.K., Rakshit, S., Sarkar, M. :

De novo genome assembly and annotation of the Arunachali yak. Sci Data 12:1027, 2025. Pubmed reference: 40533522. DOI: 10.1038/s41597-025-05362-5.

2024

Peng, W., Fu, C., Shu, S., Wang, G., Wang, H., Yue, B., Zhang, M., Liu, X., Liu, Y., Zhang, J., Zhong, J., Wang, J. :

Whole-genome resequencing of major populations revealed domestication-related genes in yaks. BMC Genomics 25:69, 2024. Pubmed reference: 38233755. DOI: 10.1186/s12864-024-09993-7.

Jiang, H., Chai, Z.X., Chen, X.Y., Zhang, C.F., Zhu, Y., Ji, Q.M., Xin, J.W. :

Yak genome database: a multi-omics analysis platform. BMC Genomics 25:346, 2024. Pubmed reference: 38580907. DOI: 10.1186/s12864-024-10274-6.

Lan, D., Fu, W., Ji, W., Mipam, T.D., Xiong, X., Ying, S., Xiong, Y., Sheng, P., Ni, J., Bai, L., Shan, T., Kong, X., Li, J. :

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks. J Anim Sci Biotechnol 15:64, 2024. Pubmed reference: 38706000. DOI: 10.1186/s40104-024-01027-2.

Guo, S., Wang, X., Zhao, S., Zhao, E. :

Whole-genome resequencing reveals the uniqueness of Subei yak. J Anim Sci 102:skae152, 2024. Pubmed reference: 38832496. DOI: 10.1093/jas/skae152.

2023

Duhan, N., Kaur, S., Kaundal, R. :

Liu, X., Liu, W., Lenstra, J.A., Zheng, Z., Wu, X., Yang, J., Li, B., Yang, Y., Qiu, Q., Liu, H., Li, K., Liang, C., Guo, X., Ma, X., Abbott, R.J., Kang, M., Yan, P., Liu, J. :

Evolutionary origin of genomic structural variations in domestic yaks. Nat Commun 14:5617, 2023. Pubmed reference: 37726270. DOI: 10.1038/s41467-023-41220-x.

Li, B., Yang, J., Liu, Y., Jiang, M. :

Genome variation map of domestic Qinghai-Tibet plateau yaks by SLAF-Seq reveals genetic footprint during artificial selection. Animals (Basel) 13:2963, 2023. Pubmed reference: 37760363. DOI: 10.3390/ani13182963.

1996

Gupta, N., Yadav, B.R., Gupta, S.C., Kumar, P., Sahai, R. :

Chromosomes of domestic yak (bos grunniens). Indian Journal of Animal Sciences 66:742-745, 1996.

Bos indicus (indicine cattle (zebu)) :

2025

Azam, S., Sahu, A., Pandey, N.K., Neupane, M., Van Tassell, C.P., Rosen, B.D., Gandham, R.K., Rath, S.N., Majumdar, S.S. :

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus. J Anim Sci Biotechnol 16:21, 2025. Pubmed reference: 39915889. DOI: 10.1186/s40104-024-01133-1.

Azam, S., Sahu, A., Pandey, N.K., Neupane, M., Van Tassell, C.P., Rosen, B.D., Gandham, R.K., Rath, S.N., Majumdar, S.S. :

Constructing a draft Indian cattle pangenome using short-read sequencing. Commun Biol 8:605, 2025. Pubmed reference: 40223124. DOI: 10.1038/s42003-025-07978-0.

Marín-Garzón, N.A., Mota, L.F.M., Vargas, G., Arikawa, L.M., Fonseca, L.F.S., Fernandes Júnior, G.A., Carvalheiro, R., Albuquerque, L.G. :

Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle. Sci Rep 15:30364, 2025. Pubmed reference: 40830176. DOI: 10.1038/s41598-025-14139-0.

Ge, F., Guo, Y., Xu, L., Low, W.Y., Ma, H., Li, Q., Wang, Z., Zhu, B., Xu, L., Gao, X., Zhang, L., Gao, H., Li, J., Chen, Y. :

The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity. DNA Res :dsaf034, 2025. Pubmed reference: 41311030. DOI: 10.1093/dnares/dsaf034.

2024

Muthusamy, P.V., Vakayil Mani, R., Kumari, S., Kaur, M., Bhaskar, B., Raghavan Pillai, R., Sajeev Kumar, T., Anilkumar, T.V., Singh, N.S. :

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle - elucidating genetic variation. Front Genet 15:1338224, 2024. Pubmed reference: 38510276. DOI: 10.3389/fgene.2024.1338224.

Benfica, L.F., Brito, L.F., do Bem, R.D., de Oliveira, L.F., Mulim, H.A., Braga, L.G., Cyrillo, J.N.S.G., Bonilha, S.F.M., Mercadante, M.E.Z. :

Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 15:1377130, 2024. Pubmed reference: 38694873. DOI: 10.3389/fgene.2024.1377130.

Tijjani, A., Kambal, S., Terefe, E., Njeru, R., Ogugo, M., Ndambuki, G., Missohou, A., Traore, A., Salim, B., Ezeasor, C., D'andre H, C., Obishakin, E.T., Diallo, B., Talaki, E., Abdoukarim, I.Y., Nash, O., Osei-Amponsah, R., Ravaorimanana, S., Issa, Y., Zegeye, T., Mukasa, C., Tiambo, C., Prendergast, J.G.D., Kemp, S.J., Han, J., Marshall, K., Hanotte, O. :

Genomic reference resource for African cattle: Genome sequences and high-density array variants. Sci Data 11:801, 2024. Pubmed reference: 39030190. DOI: 10.1038/s41597-024-03589-2.

Ayalew, W., Xiaoyun, W., Tarekegn, G.M., Naboulsi, R., Sisay Tessema, T., Van Damme, R., Bongcam-Rudloff, E., Chu, M., Liang, C., Edea, Z., Enquahone, S., Ping, Y. :

Whole genome sequences of 70 indigenous Ethiopian cattle. Sci Data 11:584, 2024. Pubmed reference: 38839789. DOI: 10.1038/s41597-024-03342-9.

S, V., D, B., Kg, T., A, G., Smk, K. :

Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India. Anim Biosci 38:395-407, 2024. Pubmed reference: 39210813. DOI: 10.5713/ab.23.0525.

2023

Rahman, J.U., Kumar, D., Singh, S.P., Shahi, B.N., Ghosh, A.K., Verma, M.K., Pathak, A., Dar, A.H., Kumar, A., Sharma, R.K. :

Genome-wide identification and annotation of SNPs and their mapping in candidate genes related to milk production and fertility traits in Badri cattle. Trop Anim Health Prod 55:117, 2023. Pubmed reference: 36928332. DOI: 10.1007/s11250-023-03535-1.

Braga, L.G., Chud, T.C.S., Watanabe, R.N., Savegnago, R.P., Sena, T.M., do Carmo, A.S., Machado, M.A., Panetto, J.C.D.C., da Silva, M.V.G.B., Munari, D.P. :

Identification of copy number variations in the genome of Dairy Gir cattle. PLoS One 18:e0284085, 2023. Pubmed reference: 37036840. DOI: 10.1371/journal.pone.0284085.

Raja, T.V., Alex, R., Singh, U., Kumar, S., Das, A.K., Sengar, G., Singh, A.K. :

Genome wide mining of SNPs and INDELs through ddRAD sequencing in Sahiwal cattle. Anim Biotechnol 34:4885-4899, 2023. Pubmed reference: 37093232. DOI: 10.1080/10495398.2023.2200517.

Powell, J., Talenti, A., Fisch, A., Hemmink, J.D., Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T.K., Morrison, L.J., Prendergast, J.G.D. :

Profiling the immune epigenome across global cattle breeds. Genome Biol 24:127, 2023. Pubmed reference: 37218021. DOI: 10.1186/s13059-023-02964-3.

Chakraborty, A., Bisht, M.S., Saxena, R., Mahajan, S., Pulikkan, J., Sharma, V.K. :

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genomics 45:1399-1408, 2023. Pubmed reference: 37231295. DOI: 10.1007/s13258-023-01401-w.

Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H.A., Wang, Y., Wang, F., Zhang, Z., Rosen, B.D., Heller, R., Jiang, Y. :

A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Res 33:1284-1298, 2023. Pubmed reference: 37714713. DOI: 10.1101/gr.277481.122.

Bos indicus x Bos taurus (hybrid cattle) :

2024

Wei, Z., Zhang, L., Gao, L., Chen, J., Peng, L., Yang, L. :

Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data. Sci Data 11:233, 2024. Pubmed reference: 38395911. DOI: 10.1038/s41597-024-03066-w.

Dang, D., Zhang, L., Gao, L., Peng, L., Chen, J., Yang, L. :

Analysis of genomic copy number variations through whole-genome scan in Yunling cattle. Front Vet Sci 11:1413504, 2024. Pubmed reference: 39104544. DOI: 10.3389/fvets.2024.1413504.

Bos primigenius (aurochs) :

2024

Erven, J.A.M., Scheu, A., Pereira Verdugo, M., Cassidy, L., Chen, N., Gehlen, B., Street, M., Madsen, O., Mullin, V.E. :

A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation. Mol Biol Evol 41:msae076, 2024. Pubmed reference: 38662789. DOI: 10.1093/molbev/msae076.

Bos taurus (taurine cattle) :

2025

Gou, Y., Jing, Y., Wang, Y., Li, X., Yang, J., Wang, K., He, H., Yang, Y., Tang, Y., Wang, C., Xu, J., Yang, F., Li, M., Tang, Q. :

AnimalGWASAtlas: annotation and prioritization of GWAS loci and quantitative trait loci for animal complex traits. J Biol Chem 301:108267, 2025. Pubmed reference: 39909383. DOI: 10.1016/j.jbc.2025.108267.

Zhang, Z., Chen, Z., Teng, J., Liu, S., Lin, Q., Wu, J., Gao, Y., Bai, Z. :

FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis. Genomics Proteomics Bioinformatics 23:qzaf006, 2025. Pubmed reference: 39932890. DOI: 10.1093/gpbjnl/qzaf006.

Ding, L., Wang, Y., Zhang, L., Luo, C., Wu, F., Huang, Y., Zhen, Y., Chen, N., Wang, L., Song, L., Pool, K., Blache, D., Maloney, S.K., Liu, D., Yang, Z., Huang, X., Li, C., Yu, X., Zhang, Z., Chen, Y., Xue, C., Gu, Y., Huang, W., Yan, L., Wei, W., Wang, Y., Zhang, J., Zhang, Y., Sun, Y., Dai, R., Wang, S., Zhao, X., Wang, H., Zhou, P., Yang, Q.Y., Wang, M. :

The HTIRDB: A resource containing a transcriptional atlas for 105 different tissues from each of seven species of domestic herbivore. Imeta 4:e267, 2025. Pubmed reference: 40027488. DOI: 10.1002/imt2.267.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Ladeira, G.C., Pinedo, P.J., Santos, J.E.P., Thatcher, W.W., Rezende, F.M. :

Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population. BMC Genomics 26:381, 2025. Pubmed reference: 40240941. DOI: 10.1186/s12864-025-11536-7.

Wang, C., Lei, B., Bao, Y., Wang, Z., Chen, C., Zhang, Y., Qin, S., Sun, T., Tang, Z., Liu, Y. :

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes. iScience 28:112049, 2025. Pubmed reference: 40104067. DOI: 10.1016/j.isci.2025.112049.

Gao, Y., Yang, L., Kuhn, K., Li, W., Zanton, G., Bowman, M., Zhao, P., Zhou, Y., Fang, L., Cole, J.B., Rosen, B.D., Ma, L., Li, C., Baldwin, R.L., Van Tassell, C.P., Zhang, Z., Smith, T.P.L., Liu, G.E. :

Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle. J Adv Res , 2025. Pubmed reference: 40258473. DOI: 10.1016/j.jare.2025.04.014.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Fang, W., Cao, Y., Liu, Y., Wu, J., Miao, L., Xiao, C., Li, X., Lv, A., Zhao, Y., Cao, Y. :

De novo genome assembly of Yanbian cattle using PacBio HiFi and Hi-C combined with RNA-seq data. Sci Data 12:1399, 2025. Pubmed reference: 40789862. DOI: 10.1038/s41597-025-05689-z.

Han, B., Li, H., Zheng, W., Zhang, Q., Chen, A., Zhu, S., Shi, T., Wang, F., Zou, D., Song, Y., Ye, W., Du, A., Fu, Y., Jia, M., Bai, Z., Yuan, Z., Liu, W., Tuo, W., Hope, J.C., MacHugh, D.E., O'Grady, J.F., Madsen, O., Sahana, G., Luo, Y., Lin, L., Li, C., Cai, Z., Li, B., Huang, J., Liu, L., Zhang, Z., Ma, Z., Hou, Y., Liu, G.E., Jiang, Y., Sun, H.Z., Fang, L., Sun, D. :

A multi-tissue single-cell expression atlas in cattle. Nat Genet 57:2546-2561, 2025. Pubmed reference: 40913183. DOI: 10.1038/s41588-025-02329-5.

Bouzeraa, L., Martin, H., Marques, J.C.S., Cerri, R., Sirard, M.A. :

Building a bovine blood DNA methylation epimap related to disease phenotypes. BMC Genomics 26:932, 2025. Pubmed reference: 41120862. DOI: 10.1186/s12864-025-12112-9.

Sorin, V., Naji, M.M., Birbes, C., Grohs, C., Escouflaire, C., Fritz, S., Eché, C., Marcuzzo, C., Suin, A., Donnadieu, C., Gaspin, C., Iampietro, C., Milan, D., Drouilhet, L., Tosser-Klopp, G., Boichard, D., Klopp, C., Sanchez, M.P., Boussaha, M. :

Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes. Genet Sel Evol 57:61, 2025. Pubmed reference: 41131485. DOI: 10.1186/s12711-025-01012-x.

Kambal, S., Walsh, A.T., Sivasankaran, S.K., Adossa, N.A., Skarlupka, J.H., Hanotte, O., Suen, G., Elsik, C.G. :

Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world. Nucleic Acids Res :gkaf1214, 2025. Pubmed reference: 41261742. DOI: 10.1093/nar/gkaf1214.

Shin, J.W., Kim, H.J., Jin, S., Chung, Y., Lee, S.H., Kim, J. :

High-quality phased genome assemblies of line-bred Korean Hanwoo cattle. Sci Data 12:1807, 2025. Pubmed reference: 41253849. DOI: 10.1038/s41597-025-06069-3.

Liu, G.E. :

Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies. J Anim Sci Biotechnol 16:158, 2025. Pubmed reference: 41287010. DOI: 10.1186/s40104-025-01294-7.

Liu, S., Yan, H., Liu, Y., Li, F., Xia, X., Wei, D., Cai, B., Lei, C., Chen, N., Ma, Y. :

Genome assembly and structural variations of Guyuan cattle. Sci Data 12:1863, 2025. Pubmed reference: 41290682. DOI: 10.1038/s41597-025-06120-3.

Johnsson, M., Johansson, A.M. :

Genome of the extinct Gotland cattle breed. BMC Genomics , 2025. Pubmed reference: 41340033. DOI: 10.1186/s12864-025-12382-3.

Ginja, C., Gao, J., Kantanen, J., Ghanem, N., Kugonza, D., Makgahlela, M., Pires, A.E., Usié, A., Dibbits, B., de Sousa, C.B., Gaspar, D., Ruvinskiy, D., Bijl, E., Smidt, H., Lindeberg, H., Bovenhuis, H., Laport, K., Pokharel, K., Blaschikoff, L., Weldenegodguad, M., Prendes, R.G., Okwasiimire, R., Guimarães, S., Lui, Y., Crooijmans, R.P.M.A. :

Whole genome sequences of 289 native cattle from Finland, the Netherlands, and Portugal. Sci Data 12:1897, 2025. Pubmed reference: 41339347. DOI: 10.1038/s41597-025-06188-x.

2024

Dorji, J., Reverter, A., Alexandre, P.A., Chamberlain, A.J., Vander-Jagt, C.J., Kijas, J., Porto-Neto, L.R. :

Ancestral alleles defined for 70 million cattle variants using a population-based likelihood ratio test. Genet Sel Evol 56:11, 2024. Pubmed reference: 38321371. DOI: 10.1186/s12711-024-00879-6.

Leonard, A.S., Mapel, X.M., Pausch, H. :

Pangenome genotyped structural variation improves molecular phenotype mapping in cattle. Genome Res 34:300-309, 2024. Pubmed reference: 38355307. DOI: 10.1101/gr.278267.123.

Beiki, H., Murdoch, B.M., Park, C.A., Kern, C., Kontechy, D., Becker, G., Rincon, G., Jiang, H., Zhou, H., Thorne, J., Koltes, J.E., Michal, J.J., Davenport, K., Rijnkels, M., Ross, P.J., Hu, R., Corum, S., McKay, S., Smith, T.P.L., Liu, W., Ma, W., Zhang, X., Xu, X., Han, X., Jiang, Z., Hu, Z.L., Reecy, J.M. :

Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience 13:giae019, 2024. Pubmed reference: 38626724. DOI: 10.1093/gigascience/giae019.

Erven, J.A.M., Scheu, A., Pereira Verdugo, M., Cassidy, L., Chen, N., Gehlen, B., Street, M., Madsen, O., Mullin, V.E. :

Smith, T., Olagunju, T., Rosen, B., Neibergs, H., Becker, G., Davenport, K., Elsik, C., Hadfield, T., Koren, S., Kuhn, K., Rhie, A., Shira, K., Skibiel, A., Stegemiller, M., Thorne, J., Villamediana, P., Cockett, N., Murdoch, B. :

The first complete T2T Assemblies of cattle and sheep Y-Chromosomes uncover remarkable divergence in structure and gene content. Res Sq , 2024. Pubmed reference: 38712074. DOI: 10.21203/rs.3.rs-4033388/v1.

Wang, Y., Huang, Y., Zhen, Y., Wang, J., Wang, L., Chen, N., Wu, F., Zhang, L., Shen, Y., Bi, C., Li, S., Pool, K., Blache, D., Maloney, S.K., Liu, D., Yang, Z., Li, C., Yu, X., Zhang, Z., Chen, Y., Xue, C., Gu, Y., Huang, W., Yan, L., Wei, W., Wang, Y., Zhang, J., Zhang, Y., Sun, Y., Wang, S., Zhao, X., Luo, C., Wang, H., Ding, L., Yang, Q.Y., Zhou, P., Wang, M. :

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Delledonne, A., Punturiero, C., Ferrari, C., Bernini, F., Milanesi, R., Bagnato, A., Strillacci, M.G. :

Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy. PLoS One 19:e0303044, 2024. Pubmed reference: 38771855. DOI: 10.1371/journal.pone.0303044.

Gao, Z., Lu, Y., Chong, Y., Li, M., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Beef cattle genome project: Advances in genome sequencing, assembly, and functional genes discovery. Int J Mol Sci 25:7147, 2024. Pubmed reference: 39000250. DOI: 10.3390/ijms25137147.

Genomic reference resource for African cattle: Genome sequences and high-density array variants. Sci Data 11:801, 2024. Pubmed reference: 39030190. DOI: 10.1038/s41597-024-03589-2.

Chang, W.J., Baker, M.S., Laritsky, E., Gunasekara, C.J., Maduranga, U., Galliou, J.C., McFadden, J.W., Waltemyer, J.R., Berggren-Thomas, B., Tate, B.N., Zhang, H., Rosen, B.D., Van Tassell, C.P., Liu, G.E., Coarfa, C., Ren, Y.A., Waterland, R.A. :

Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol 25:185, 2024. Pubmed reference: 39004763. DOI: 10.1186/s13059-024-03307-6.

Ayalew, W., Xiaoyun, W., Tarekegn, G.M., Naboulsi, R., Sisay Tessema, T., Van Damme, R., Bongcam-Rudloff, E., Chu, M., Liang, C., Edea, Z., Enquahone, S., Ping, Y. :

Whole genome sequences of 70 indigenous Ethiopian cattle. Sci Data 11:584, 2024. Pubmed reference: 38839789. DOI: 10.1038/s41597-024-03342-9.

Boschiero, C., Neupane, M., Yang, L., Schroeder, S.G., Tuo, W., Ma, L., Baldwin, R.L., Van Tassell, C.P., Liu, G.E. :

A pilot detection and associate study of gene presence-absence variation in Holstein cattle. Animals (Basel) 14:1921, 2024. Pubmed reference: 38998033. DOI: 10.3390/ani14131921.

Jin, S., Won, J.I., Kim, H.J., Park, B., Kim, S.W., Kim, U.H., Kang, S.S., Lee, H.J., Moon, S.J., Park, M.S., Sim, Y.T., Jang, S.S., Kim, N.Y. :

Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle. J Anim Sci Technol 66:717-725, 2024. Pubmed reference: 39165748. DOI: 10.5187/jast.2024.e10.

Olagunju, T.A., Rosen, B.D., Neibergs, H.L., Becker, G.M., Davenport, K.M., Elsik, C.G., Hadfield, T.S., Koren, S., Kuhn, K.L., Rhie, A., Shira, K.A., Skibiel, A.L., Stegemiller, M.R., Thorne, J.W., Villamediana, P., Cockett, N.E., Murdoch, B.M., Smith, T.P.L. :

Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nat Commun 15:8277, 2024. Pubmed reference: 39333471. DOI: 10.1038/s41467-024-52384-5.

Su, R., Zhou, H., Yang, W., Moqir, S., Ritu, X., Liu, L., Shi, Y., Dong, A., Bayier, M., Letu, Y., Manxi, X., Chulu, H., Nasenochir, N., Meng, H., Herrid, M. :

Near telomere-to-telomere genome assembly of Mongolian cattle: implications for population genetic variation and beef quality. Gigascience 13:giae099, 2024. Pubmed reference: 39693631. DOI: 10.1093/gigascience/giae099.

Grant, J.R., Herman, E.K., Barlow, L.D., Miglior, F., Schenkel, F.S., Baes, C.F., Stothard, P. :

A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application. BMC Genomics 25:903, 2024. Pubmed reference: 39350025. DOI: 10.1186/s12864-024-10812-2.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. Nucleic Acids Res 51:D1388-D1396, 2023. Pubmed reference: 36062570. DOI: 10.1093/nar/gkac750.

Sasaki, S., Haga, Y., Wakaguri, H., Abe, K., Suzuki, Y. :

De novo genome assembly of Japanese Black cattle as model of an economically relevant animal. Methods Mol Biol 2632:41-55, 2023. Pubmed reference: 36781720. DOI: 10.1007/978-1-0716-2996-3_4.

Liu, Y., Mu, Y., Wang, W., Ahmed, Z., Wei, X., Lei, C., Ma, Z. :

Analysis of genomic copy number variations through whole-genome scan in Chinese Qaidam cattle. Front Vet Sci 10:1148070, 2023. Pubmed reference: 37065216. DOI: 10.3389/fvets.2023.1148070.

Lee, Y.L., Bosse, M., Takeda, H., Moreira, G.C.M., Karim, L., Druet, T., Oget-Ebrad, C., Coppieters, W., Veerkamp, R.F., Groenen, M.A.M., Georges, M., Bouwman, A.C., Charlier, C. :

High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data. BMC Genomics 24:225, 2023. Pubmed reference: 37127590. DOI: 10.1186/s12864-023-09259-8.

Cai, W., Zhang, Y., Chang, T., Wang, Z., Zhu, B., Chen, Y., Gao, X., Xu, L., Zhang, L., Gao, H., Song, J., Li, J. :

The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle. J Anim Sci Biotechnol 14:78, 2023. Pubmed reference: 37165455. DOI: 10.1186/s40104-023-00876-7.

Leonard, A.S., Crysnanto, D., Mapel, X.M., Bhati, M., Pausch, H. :

Graph construction method impacts variation representation and analyses in a bovine super-pangenome. Genome Biol 24:124, 2023. Pubmed reference: 37217946. DOI: 10.1186/s13059-023-02969-y.

Powell, J., Talenti, A., Fisch, A., Hemmink, J.D., Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T.K., Morrison, L.J., Prendergast, J.G.D. :

Profiling the immune epigenome across global cattle breeds. Genome Biol 24:127, 2023. Pubmed reference: 37218021. DOI: 10.1186/s13059-023-02964-3.

Salavati, M., Clark, R., Becker, D., Kühn, C., Plastow, G., Dupont, S., Moreira, G.C.M., Charlier, C., Clark, E.L. :

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing. G3 (Bethesda) 13:jkad108, 2023. Pubmed reference: 37216666. DOI: 10.1093/g3journal/jkad108.

Eché, C., Iampietro, C., Birbes, C., Dréau, A., Kuchly, C., Di Franco, A., Klopp, C., Faraut, T., Djebali, S., Castinel, A., Zytnicki, M., Denis, E., Boussaha, M., Grohs, C., Boichard, D., Gaspin, C., Milan, D., Donnadieu, C. :

A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling. Sci Data 10:369, 2023. Pubmed reference: 37291142. DOI: 10.1038/s41597-023-02249-1.

Melzer, N., Qanbari, S., Ding, X., Wittenburg, D. :

CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map. Front Genet 14:1082782, 2023. Pubmed reference: 37323679. DOI: 10.3389/fgene.2023.1082782.

Smith, T.P.L., Bickhart, D.M., Boichard, D., Chamberlain, A.J., Djikeng, A., Jiang, Y., Low, W.Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., Schnabel, R.D., Rosen, B.D. :

The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biol 24:139, 2023. Pubmed reference: 37337218. DOI: 10.1186/s13059-023-02975-0.

Triant, D.A., Walsh, A.T., Hartley, G.A., Petry, B., Stegemiller, M.R., Nelson, B.M., McKendrick, M.M., Fuller, E.P., Cockett, N.E., Koltes, J.E., McKay, S.D., Green, J.A., Murdoch, B.M., Hagen, D.E., Elsik, C.G. :

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Jang, J., Jung, J., Lee, Y.H., Lee, S., Baik, M., Kim, H. :

Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies. Sci Data 10:560, 2023. Pubmed reference: 37612339. DOI: 10.1038/s41597-023-02453-z.

Yuan, C., Tang, L., Lopdell, T., Petrov, V.A., Oget-Ebrad, C., Moreira, G.C.M., Gualdrón Duarte, J.L., Sartelet, A., Cheng, Z., Salavati, M., Wathes, C.D., Crowe, M.A. :

An organism-wide ATAC-seq peak catalogue for the bovine and its use to identify regulatory variants. Genome Res 33:1848-1864, 2023. Pubmed reference: 37751945. DOI: 10.1101/gr.277947.123.

Li, T.T., Xia, T., Wu, J.Q., Hong, H., Sun, Z.L., Wang, M., Ding, F.R., Wang, J., Jiang, S., Li, J., Pan, J., Yang, G., Feng, J.N., Dai, Y.P., Zhang, X.M., Zhou, T., Li, T. :

De novo genome assembly depicts the immune genomic characteristics of cattle. Nat Commun 14:6601, 2023. Pubmed reference: 37857610. DOI: 10.1038/s41467-023-42161-1.

2022

Yang, L., Gao, Y., Li, M., Park, K.E., Liu, S., Kang, X., Liu, M., Oswalt, A., Fang, L., Telugu, B.P., Sattler, C.G., Li, C.J., Cole, J.B., Seroussi, E., Xu, L., Yang, L., Zhou, Y., Li, L., Zhang, H., Rosen, B.D., Van Tassell, C.P., Ma, L., Liu, G.E. :

Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics 23:181, 2022. Pubmed reference: 35247961. DOI: 10.1186/s12864-022-08415-w.

Raz, R., Roth, Z., Gershoni, M. :

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples. Sci Data 9:469, 2022. Pubmed reference: 35918364. DOI: 10.1038/s41597-022-01597-8.

2021

Heaton, M.P., Smith, T.P.L., Bickhart, D.M., Vander Ley, B.L., Kuehn, L.A., Oppenheimer, J., Shafer, W.R., Schuetze, F.T., Stroud, B., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Rosen, B.D. :

A reference genome assembly of Simmental cattle, Bos taurus taurus. J Hered 112:184-91, 2021. Pubmed reference: 33438035. DOI: 10.1093/jhered/esab002.

Erratum to: A reference genome assembly of Simmental cattle, Bos taurus taurus. J Hered 112:565, 2021. Pubmed reference: 34436588. DOI: 10.1093/jhered/esab039.

MacPhillamy, C., Pitchford, W.S., Alinejad-Rokny, H., Low, W.Y. :

Opportunity to improve livestock traits using 3D genomics. Anim Genet 52:785-798, 2021. Pubmed reference: 34494283. DOI: 10.1111/age.13135.

Neumann, G.B., Korkuć, P., Arends, D., Wolf, M.J., May, K., Reißmann, M., Elzaki, S., König, S., Brockmann, G.A. :

Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN). BMC Genomics 22:905, 2021. Pubmed reference: 34922441. DOI: 10.1186/s12864-021-08237-2.

2020

De Lorenzi, L., Parma, P. :

Identification of Some Errors in the Genome Assembly of Bovidae by FISH. Cytogenet Genome Res 160:85-93, 2020. Pubmed reference: 32235117. DOI: 10.1159/000506221.

Rosen, B.D., Bickhart, D.M., Schnabel, R.D., Koren, S., Elsik, C.G., Tseng, E., Rowan, T.N., Low, W.Y., Zimin, A., Couldrey, C., Hall, R., Li, W., Rhie, A., Ghurye, J., McKay, S.D., Thibaud-Nissen, F., Hoffman, J., Murdoch, B.M., Snelling, W.M., McDaneld, T.G., Hammond, J.A., Schwartz, J.C., Nandolo, W., Hagen, D.E., Dreischer, C., Schultheiss, S.J., Schroeder, S.G., Phillippy, A.M., Cole, J.B., Van Tassell, C.P., Liu, G., Smith, T.P.L., Medrano, J.F. :

De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience 9:giaa021, 2020. Pubmed reference: 32191811. DOI: 10.1093/gigascience/giaa021.

Triant, D.A., Le Tourneau, J.J., Diesh, C.M., Unni, D.R., Shamimuzzaman, M., Walsh, A.T., Gardiner, J., Goldkamp, A.K., Li, Y., Nguyen, H.N., Roberts, C., Zhao, Z., Alexander, L.J., Decker, J.E., Schnabel, R.D., Schroeder, S.G., Sonstegard, T.S., Taylor, J.F., Rivera, R.M., Hagen, D.E., Elsik, C.G. :

Using online tools at the Bovine Genome Database to manually annotate genes in the new reference genome. Anim Genet 51:675-682, 2020. Pubmed reference: 32537769. DOI: 10.1111/age.12962.

2019

Sasaki, S., Muraki, E., Inoue, Y., Suezawa, R., Nikadori, H., Yoshida, Y., Nariai, S., Hideshima, R., Moriwaki, S., Nakashima, R., Uchiyama, K., Yoshinari, K., Takeda, M., Kojima, T. :

Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle. Anim Sci J 90:1503-1509, 2019. Pubmed reference: 31599477. DOI: 10.1111/asj.13293.

Womack, J.E.J. :

Mapping Genes Is Good for You. Annu Rev Anim Biosci 7:1-16, 2019. Pubmed reference: 30296836. DOI: 10.1146/annurev-animal-020518-114902.

2015

Ma, L., O'Connell, J.R., VanRaden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G.E., Da, Y., Wiggans, G.R. :

Cattle sex-specific recombination and genetic control from a large pedigree analysis. PLoS Genet 11:e1005387, 2015. Pubmed reference: 26540184. DOI: 10.1371/journal.pgen.1005387.

2013

Kõks, S., Lilleoja, R., Reimann, E., Salumets, A., Reemann, P., Jaakma, Ü. :

Sequencing and annotated analysis of the Holstein cow genome. Mamm Genome 24:309-21, 2013. Pubmed reference: 23893136. DOI: 10.1007/s00335-013-9464-0.

2012

Boichard, D., Chung, H., Dassonneville, R., David, X., Eggen, A., Fritz, S., Gietzen, K.J., Hayes, B.J., Lawley, C.T., Sonstegard, T.S., Van Tassell, C.P., VanRaden, P.M., Viaud-Martinez, K.A., Wiggans, G.R. :

Design of a bovine low-density SNP array optimized for imputation. PLoS One 7:e34130, 2012. Pubmed reference: 22470530. DOI: 10.1371/journal.pone.0034130.

2011

Stothard, P., Choi, J.W., Basu, U., Sumner-Thomson, J.M., Meng, Y., Liao, X., Moore, S.S. :

Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12:559, 2011. Pubmed reference: 22085807. DOI: 10.1186/1471-2164-12-559.

Rincon, G., Weber, K.L., Eenennaam, A.L., Golden, B.L., Medrano, J.F. :

Hot topic: performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 94:6116-21, 2011. Pubmed reference: 22118099. DOI: 10.3168/jds.2011-4764.

2009

Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marçais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. :

A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10:R42, 2009. Pubmed reference: 19393038. DOI: 10.1186/gb-2009-10-4-r42.

Liu, Y., Qin, X., Song, X.Z., Jiang, H., Shen, Y., Durbin, K.J., Lien, S., Kent, M.P., Sodeland, M., Ren, Y., Zhang, L., Sodergren, E., Havlak, P., Worley, K.C., Weinstock, G.M., Gibbs, R.A. :

Bos taurus genome assembly. BMC Genomics 10:180, 2009. Pubmed reference: 19393050. DOI: 10.1186/1471-2164-10-180.

Bovine Genome Sequencing and Analysis Consortium :

The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522-8, 2009. Pubmed reference: 19390049. DOI: 10.1126/science.1169588.

Eck, S.H., Benet-Pagès, A., Flisikowski, K., Meitinger, T., Fries, R., Strom, T.M. :

Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol 10:R82, 2009. Pubmed reference: 19660108. DOI: 10.1186/gb-2009-10-8-r82.

Bovine HapMap Consortium et al. :

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-32, 2009. Pubmed reference: 19390050. DOI: 10.1126/science.1167936.

Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. :

Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350, 2009. Pubmed reference: 19390634. DOI: 10.1371/journal.pone.0005350.

2008

Charlier, C., Coppieters, W., Rollin, F., Desmecht, D., Agerholm, JS., Cambisano, N., Carta, E., Dardano, S., Dive, M., Fasquelle, C., Frennet, JC., Hanset, R., Hubin, X., Jorgensen, C., Karim, L., Kent, M., Harvey, K., Pearce, BR., Simon, P., Tama, N., Nie, H., Vandeputte, S., Lien, S., Longeri, M., Fredholm, M., Harvey, RJ., Georges, M. :

Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat Genet 40:449-54, 2008. Pubmed reference: 18344998. DOI: 10.1038/ng.96.

Van Tassell, C.P., Smith, T.P., Matukumalli, L.K., Taylor, J.F., Schnabel, R.D., Lawley, C.T., Haudenschild, C.D., Moore, S.S., Warren, W.C., Sonstegard, T.S. :

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5:247-52, 2008. Pubmed reference: 18297082. DOI: 10.1038/nmeth.1185.

2007

Snelling, W.M., Chiu, R., Schein, J.E., Hobbs, M., Abbey, C.A., Adelson, D.L., Aerts, J., Bennett, G.L., Bosdet, I.E., Boussaha, M., Brauning, R., Caetano, A.R., Costa, M.M., Crawford, A.M., Dalrymple, B.P., Eggen, A., Everts-van der Wind, A., Floriot, S., Gautier, M., Gill, C.A., Green, R.D., Holt, R., Jann, O., Jones, S.J., Kappes, S.M., Keele, J.W., de Jong, P.J., Larkin, D.M., Lewin, H.A., McEwan, J.C., McKay, S., Marra, M.A., Mathewson, C.A., Matukumalli, L.K., Moore, S.S., Murdoch, B., Nicholas, F.W., Osoegawa, K., Roy, A., Salih, H., Schibler, L., Schnabel, R.D., Silveri, L., Skow, L.C., Smith, T.P., Sonstegard, T.S., Taylor, J.F., Tellam, R., Van Tassell, C.P., Williams, J.L., Womack, J.E., Wye, N.H., Yang, G., Zhao, S. :

A physical map of the bovine genome. Genome Biol 8:R165, 2007. Pubmed reference: 17697342. DOI: 10.1186/gb-2007-8-8-r165.

2006

Womack, J.E. :

The bovine genome. Genome Dyn 2:69-78, 2006. Pubmed reference: 18753770. DOI: 10.1159/000095095.

Jann, O.C., Aerts, J., Jones, M., Hastings, N., Law, A., McKay, S., Marques, E., Prasad, A., Yu, J., Moore, S.S., Floriot, S., Mahé, M.F., Eggen, A., Silveri, L., Negrini, R., Milanesi, E., Ajmone-Marsan, P., Valentini, A., Marchitelli, C., Savarese, M.C., Janitz, M., Herwig, R., Hennig, S., Gorni, C., Connor, E.E., Sonstegard, T.S., Smith, T., Drögemüller, C., Williams, J.L. :

A second generation radiation hybrid map to aid the assembly of the bovine genome sequence. BMC Genomics 7:283, 2006. Pubmed reference: 17087818. DOI: 10.1186/1471-2164-7-283.

Weikard, R., Goldammer, T., Laurent, P., Womack, J.E., Kuehn, C. :

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits. BMC Genomics 7:53, 2006. Pubmed reference: 16542434. DOI: 10.1186/1471-2164-7-53.

2003

Larkin, D.M., Everts-van, der, Wind, A., Rebeiz, M., Schweitzer, P.A., Bachman, S., Green, C., Wright, C.L., Campos, E.J., Benson, L.D., Edwards, J., Liu, L., Osoegawa, K., Womack, J.E., de, Jong, P.J., Lewin, H.A. :

A cattle-human comparative map built with cattle BAC-ends and human genome sequence Genome Research 13:1966-72, 2003. Pubmed reference: 12902387. DOI: 10.1101/gr.1560203.

2002

Weikard, R., Kuhn, C., Goldammer, T., Laurent, P., Womack, J.E., Schwerin, M. :

Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping Genomics 79:768-776, 2002. Pubmed reference: 12036290. DOI: 10.1006/geno.2002.6778.

Gautier, M., Hayes, H., Eggen, A. :

An extensive and comprehensive radiation hybrid map of bovine Chromosome 15: comparison with human Chromosome 11 Mammalian Genome 13:316-319, 2002. Pubmed reference: 12115035. DOI: 10.1007/s00335-001-3069-8.

Schlapfer, J., Stahlberger-Saitbekova, N., Comincini, S., Gaillard, C., Hills, D., Meyer, R.K., Williams, J.L., Womack, J., Zurbriggen, A., Dolf, G. :

A higher resolution radiation hybrid map of bovine chromosome 13 Genetics Selection Evolution 34:255-267, 2002.

Drogemuller, C., Bader, A., Wohlke, A., Kuiper, H., Leeb, T., Distl, O. :

A high-resolution comparative RH map of the proximal part of bovine chromosome 1 Animal Genetics 33:271-279, 2002. Pubmed reference: 12139506.

Williams, J.L., Eggen, A., Ferretti, L., Farr, C.J., Gautier, M., Amati, G., Ball, G., Caramorr, T., Critcher, R., Costa, S., Hextall, P., Hills, D., Jeulin, A., Kiguwa, S.L., Ross, O., Smith, A.L., Saunier, K., Urquhart, B., Waddington, D. :

A bovine whole-genome radiation hybrid panel and outline map Mammalian Genome 13:469-474, 2002. Pubmed reference: 12226714. DOI: 10.1007/s00335-002-3001-x.

Jiang, Z.H., Melville, J.S., Cao, H.H., Kumar, S., Filipski, A., Gibbins, A.M.V. :

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome Genome 45:769-776, 2002. Pubmed reference: 12175081.

Reed, K.M., Ihara, N., Mariani, P., Mendoza, K.M., Jensen, L.E., Bellavia, R., de, Leon, F.A.P., Bennett, G.L., Sugimoto, Y., Beattie, C.W. :

High-resolution genetic map of bovine chromosome 29 through focused marker development Cytogenetic & Genome Research 96:210-216, 2002.

Antoniou, E., Gallagher, D., Taylor, J., Davis, S., Womack, J., Grosz, M. :

A comparative map of bovine chromosome 25 with human chromosomes 7 and 16 Cytogenetic & Genome Research 97:128-132, 2002.

Liu, W.S., Mariani, P., Beattie, C.W., Alexander, L.J., Ponce, De, Leon, F.A. :

A radiation hybrid map for the bovine Y Chromosome Mammalian Genome 13:320-6, 2002. Pubmed reference: 12115036. DOI: 10.1007/s00335-001-2133-8.

2001

Sonstegard, T.S., Bennett, G.L., Kalm, E., Kappes, S.M., Lewin, H.A., Olsaker, I., Schmutz, S., Thomsen, H., Vage, D.I., Van, Tassell, C.P., Xu, N. :

Consensus and comprehensive linkage maps of bovine chromosome 25 Animal Genetics 32:114-115, 2001. Pubmed reference: 11421953.

2000

Vage, D.I., Olsaker, I., Klungland, H., Gomez-Raya, L., Lien, S. :

A male genetic map designed for quantitative trait loci mapping in Norwegian cattle Acta Agriculturae Scandinavica Section A-Animal Science 50:56-63, 2000.

Ozawa, A., Band, M.R., Larson, J.H., Donovan, J., Green, C.A., Womack, J.E., Lewin, H.A. :

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping Proceedings of the National Academy of Sciences of the United States of America 97:4150-4155, 2000. Pubmed reference: 10737760. DOI: 10.1073/pnas.050007097.

Amarante, M.R.V., Yang, Y.P., Kata, S.R., Lopes, C.R., Womack, J.E. :

RH maps of bovine chromosomes 15 and 29: conservation of human chromosomes 11 and 5 Mammalian Genome 11:364-368, 2000. Pubmed reference: 10790535.

Band, M.R., Larson, J.H., Rebeiz, M., Green, C.A., Heyen, D.W., Donovan, J., Windish, R., Steining, C., Mahyuddin, P., Womack, J.E., Lewin, H.A. :

An ordered comparative map of the cattle and human genomes Genome Research 10:1359-1368, 2000. Pubmed reference: 10984454.

1999

Rexroad, C.E., Schlapfer, J.S., Yang, Y., Harlizius, B., Womack, J.E. :

A radiation hybrid map of bovine chromosome one Animal Genetics 30:325-332, 1999. Pubmed reference: 10582277.

Rexroad, C.E., Womack, J.E. :

Parallel RH mapping of BTA1 with HSA3 and HSA21 Mammalian Genome 10:1095-1097, 1999. Pubmed reference: 10556430.

Gu, Z., Womack, J.E., Kirkpatrick, B.W. :

A radiation hybrid map of bovine chromosome 7 and comparative mapping with human chromosome 19 p arm Mammalian Genome 10:1112-1114, 1999. Pubmed reference: 10556435.

1998

Yang, Y.P., Rexroad, C.E., Schlapfer, J., Womack, J.E. :

An integrated radiation hybrid map of bovine chromosome 19 and ordered comparative mapping with human chromosome 17 Genomics 48:93-99, 1998. Pubmed reference: 9503021. DOI: 10.1006/geno.1997.5143.

Yang, Y.P., Womack, J.E. :

Parallel radiation hybrid mapping - a powerful tool for high-resolution genomic comparison Genome Research 8:731-736, 1998. Pubmed reference: 9685320.

Band, M., Larson, J.H., Womack, J.E., Lewin, H.A. :

A radiation hybrid map of BTA23 - identification of a chromosomal rearrangement leading to separation of the cattle mhc class ii subregions Genomics 53:269-275, 1998. Pubmed reference: 9799592. DOI: 10.1006/geno.1998.5507.

1997

Barendse, W., Vaiman, D., Kemp, S.J., Sugimoto, Y., Armitage, S.M., Williams, J.L., Sun, H.S., Eggen, A., Agaba, M., Aleyasin, S.A., Band, M., Bishop, M.D., Buitkamp, J., Byrne, K., Collins, F., Cooper, L., Coppettiers, W., Denys, B., Drinkwater, R.D., Easterday, K., Elduque, C., Ennis, S., Erhardt, G., Ferretti, L., Flavin, N., et al. :

A medium-density genetic linkage map of the bovine genome Mamm Genome 8:21-8, 1997. Pubmed reference: 9021143. DOI: 10.1007/s003359900340.

Ferretti, L., Urquhart, B.G.D., Eggen, A., Olsaker, I., Harlizius, B., Castiglioni, B., Mezzelani, A., Toldo, S.S., Thieven, U., Zhang, Y., Morgan, A.L.G., Teres, V.M., Schwerin, M., Martinburriel, I., Chowdhary, B.P., Erhardt, G., Nijman, I.J., Cribiu, E.P., Barendse, W., Leveziel, H., Fries, R., Williams, J.L. :

Cosmid-derived markers anchoring the bovine genetic map to the physical map Mammalian Genome 8:29-36, 1997. Pubmed reference: 9021144.

Sonstegard, T.S., Lopezcorrales, N.L., Kappes, S.M., Stone, R.T., Ambady, S., Deleon, F.A.P., Beattie, C.W. :

An integrated genetic and physical map of the bovine x chromosome Mammalian Genome 8:16-20, 1997. Pubmed reference: 9021142.

Kappes, S.M., Keele, J.W., Stone, R.T., Sonstegard, T.S., Smith, T.P.L., Mcgraw, R.A., Lopezcorrales, N.L., Beattie, C.W. :

A second-generation linkage map of the bovine genome Genome Res 7:235-49, 1997. Pubmed reference: 9074927. DOI: 10.1101/gr.7.3.235.

Kalm, E. :

Genome mapping by cattle [German] Archiv fur Tierzucht-Archives of Animal Breeding 40:74-79, 1997.

Smith, T.P.L., Lopezcorrales, N., Grosz, M.D., Beattie, C.W., Kappes, S.M. :

Anchoring of bovine chromosomes 4, 6, 7, 10, and 14 linkage group telomeric ends via fish analysis of lambda clones Mammalian Genome 8:333-336, 1997. Pubmed reference: 9107677.

Beever, J.E., Fisher, S.R., Guerin, G., Lewin, H.A. :

Mapping of eight human chromosome 1 orthologs to cattle chromosomes 3 and 16 Mammalian Genome 8:533-536, 1997. Pubmed reference: 9196004.

Agaba, M.K., Kemp, S.J., Barendse, W., Teale, A. :

Comparative mapping in cattle of genes located on human chromosome 18 Mammalian Genome 8:530-532, 1997. Pubmed reference: 9196003.

Barendse, W. :

A medium density genetic linkage map of the bovine genome (vol 8, pg 21, 1997) Mammalian Genome 8:798, 1997.

Womack, J.E., Johnson, J.S., Owens, E.K., Rexroad, C.E., Schlapfer, J., Yang, Y.P. :

A whole-genome radiation hybrid panel for bovine gene mapping Mammalian Genome 8:854-856, 1997. Pubmed reference: 9337401.

Choudhury, A., Das, D., Goswami, R.N. :

Chromosome complements of male assam cattle (bos indicus) and pure jersey bulls (bos taurus). Indian Journal of Animal Sciences 67:63-66, 1997.

Iannuzzi, L., Dimeo, G.P., Perucatti, A. :

The high resolution GBA plus CBA-banded karyotype in cattle (Bos taurus l). Caryologia 50:59-66, 1997.

1996

Chowdhary, B.P., Fronicke, L., Gustavsson, I., Scherthan, H. :

Comparative analysis of the cattle and human genomes - detection of zoo-FISH and gene mapping-based chromosomal homologies Mammalian Genome 7:297-302, 1996. Pubmed reference: 8661702.

Beever, J.E., Lewin, H.A., Barendse, W., Andersson, L., Armitage, S.M., Beattie, C.W., Burns, B.M., Davis, S.K., Kappes, S.M., Kirkpatrick, B.W., Ma, R.Z., Mcgraw, R.A., Stone, R.T., Taylor, J.F. :

Report of the first workshop on the genetic map of bovine chromosome 23 Animal Genetics 27:69-75, 1996. Pubmed reference: 8856895.

Ma, R.Z., Beever, J.E., Da, Y., Green, C.A., Russ, I., Park, C., Heyen, D.W., Everts, R.E., Fisher, S.R., Overton, K.M., Teale, A.J., Kemp, S.J., Hines, H.C., Guerin, G., Lewin, H.A. :

A male linkage map of the cattle (bos taurus) genome Journal of Heredity 87:261-271, 1996. Pubmed reference: 8776874.

Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., Brown, S., Burt, D., Charlier, C., Copeland, N., Davis, S., Davisson, M., Edwards, J., Eggen, A., Elgar, G., Eppig, J.T., Franklin, I., Grewe, P., Gill, T., Graves, J.A.M., Hawken, R., Hetzel, J., Hillyard, A., Jacob, H., Jaswinska, L., Jenkins, N., Kunz, H., Levan, G., Lie, O., Lyons, L., Maccarone, P., Mellersh, C., Montgomery, G., Moore, S., Moran, C., Morizot, D., Neff, M., Nicholas, F.W., O'Brien, S.J., Parsons, Y., Peters, J., Postlethwait, J., Raymond, M., Rothschild, M., Schook, L., Sugimoto, Y., Szpirer, C., Tate, M., Taylor, J., Vandeberg, J., Wakefield, M., Wienberg, J., Womack, J. :

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

Mezzelani, A., Castiglioni, B., Eggen, A., Ferretti, L. :

T-banding pattern of bovine chromosomes and karyotype reconstitution with physically mapped cosmids. Cytogenet Cell Genet 73:229-34, 1996. Pubmed reference: 8697814. DOI: 10.1159/000134345.

Iannuzzi, L., Gallagher, D.S., Womack, J.E., Meo, G.P., Shelling, C.P., Groenen, M.A. :

FISH mapping of the alpha-S2 casein gene on river buffalo and cattle chromosomes identifies a nomenclature discrepancy in the bovine karyotype. Chromosome Res 4:159-62, 1996. Pubmed reference: 8785611. DOI: 10.1007/BF02259710.

Iannuzzi, L. :

G- and R-banded prometaphase karyotypes in cattle (Bos taurus L.). Chromosome Res 4:448-56, 1996. Pubmed reference: 8889244. DOI: 10.1007/BF02265052.

Popescu, C.P., Long, S., Riggs, P., Womack, J., Schmutz, S., Fries, R., Gallagher, D.S. :

Standardization of cattle karyotype nomenclature: report of the committee for the standardization of the cattle karyotype. Cytogenet Cell Genet 74:259-61, 1996. Pubmed reference: 8976379. DOI: 10.1159/000134429.

Kawarsky, S.J., Basrur, P.K., Stubbings, R.B., Hansen, P.J., King, W.A. :

Chromosomal abnormalities in bovine embryos and their influence on development. Biol Reprod 54:53-9, 1996. Pubmed reference: 8838000. DOI: 10.1095/biolreprod54.1.53.

Choudhury, A., Das, D., Goswami, R.N., Das, B. :

Studies on karyotypes of assam local cattle. Indian Veterinary Journal 73:41-45, 1996.

Tambasco, A.J., Deoliveira, M.C.S., Rocha, A., Tambasco, D.D., Denovaes, A.P. :

Effects of enzootic bovine leukosis virus on the chromosomes of purebred holstein and holstein-zebu cows. Arquivos de Biologia e Tecnologia 39:855-859, 1996.

Vijh, R.K., Tantia, M.S., Vij, P.K., Kumar, P., Sahai, R. :

Sister chromatid differentiation in Rathi cattle. Indian Journal of Animal Sciences 66:83-85, 1996.

1995

Hawkins, G.A., Toldo, S.S., Bishop, M.D., Kappes, S.M., Fries, R., Beattie, C.W. :

Physical and linkage mapping of the bovine genome with cosmids Mammalian Genome 6:249-254, 1995. Pubmed reference: 7613028.

Eggen, A., Fries, R. :

An integrated cytogenetic and meiotic map of the bovine genome Animal Genetics 26:215-236, 1995. Pubmed reference: 7661394.

Georges, M., Nielsen, D., Mackinnon, M., Mishra, A., Okimoto, R., Pasquino, A.T., Sargeant, L.S., Sorensen, A., Steele, M.R., Zhao, X. :

Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139:907-20, 1995. Pubmed reference: 7713441.

Iannuzzi, L., Di Meo, G.P. :

Chromosomal evolution in bovids: a comparison of cattle, sheep and goat G- and R-banded chromosomes and cytogenetic divergences among cattle, goat and river buffalo sex chromosomes. Chromosome Res 3:291-9, 1995. Pubmed reference: 7551543. DOI: 10.1007/BF00713067.

Schmitz, A., Oustry, A., Chaput, B., Bahri-Darwich, I., Yerle, M., Millan, D., Frelat, G., Cribiu, E.P. :

The bovine bivariate flow karyotype and peak identification by chromosome painting with PCR-generated probes. Mamm Genome 6:415-20, 1995. Pubmed reference: 7647464. DOI: 10.1007/BF00355643.

Solinas-Toldo, S., Mezzelani, A., Hawkins, G.A., Bishop, M.D., Olsaker, I., Mackinlay, A., Ferretti, L., Fries, R. :

Combined Q-banding and fluorescence in situ hybridization for the identification of bovine chromosomes 1 to 7. Cytogenet Cell Genet 69:1-6, 1995. Pubmed reference: 7835074. DOI: 10.1159/000133925.

Hidas, A. :

Heterochromatin heterogeneity revealed by restriction endonuclease digestion and subsequent C-banding on bovine metaphase chromosomes. Hereditas 122:285-8, 1995. Pubmed reference: 8537244. DOI: 10.1111/j.1601-5223.1995.00285.x.

King, W.A., Supplizi, A.V., Diop, H.E.P., Bousquet, D. :

Chromosomal analysis of embryos produced by artificially inseminated superovulated cattle. Genetics Selection Evolution 27:189-194, 1995.

1994

Bishop, M.D., Kappes, S.M., Keele, J.W., Stone, R.T., Sunden, S.L.F., Hawkins, G.A., Toldo, S.S., Fries, R., Grosz, M.D., Yoo, J.Y., Beattie, C.W. :

A Genetic Linkage Map for Cattle Genetics 136:619-639, 1994. Pubmed reference: 7908653.

Barendse, W., Armitage, S.M., Kossarek, L.M., Shalom, A., Kirkpatrick, B.W., Ryan, A.M., Clayton, D., Li, L., Neibergs, H.L., Zhang, N., Grosse, W.M., Weiss, J., Creighton, P., Mccarthy, F., Ron, M., Teale, A.J., Fries, R., Mcgraw, R.A., Moore, S.S., Georges, M., Soller, M., Womack, J.E., Hetzel, D.J.S. :

A Genetic Linkage Map of the Bovine Genome Nature Genetics 6:227-235, 1994. Pubmed reference: 8012383. DOI: 10.1038/ng0394-227.

Echard, G., Broad, T.E., Hill, D., Pearce, P. :

Present Status of the Ovine Gene Map (Ovis aries) - Comparison with the Bovine Map (Bos taurus) Mammalian Genome 5:324-332, 1994. Pubmed reference: 8043945.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

Kaftanovskaya, H.M., Serov, O.L. :

High-resolution GTG-banded chromosomes of cattle, sheep, and goat: a comparative study. J Hered 85:395-400, 1994. Pubmed reference: 7963454. DOI: 10.1093/oxfordjournals.jhered.a111485.

Gallagher, D.S., Derr, J.N., Womack, J.E. :

Chromosome conservation among the advanced pecorans and determination of the primitive bovid karyotype. J Hered 85:204-10, 1994. Pubmed reference: 8014460. DOI: 10.1093/oxfordjournals.jhered.a111436.

Sahoo, A.K., Choudhuri, G., Koley, N. :

Studies on the Metaphase Chromosomes of Crossbred Cattle of Divergent Exotic Inheritance. Indian Veterinary Journal 71:939-940, 1994.

Sarkhel, B.C., Katpatal, B.G. :

Heteromorphism of homologus chromosomes in pure and crossbred cattle. Indian Journal of Animal Sciences 64:849-852, 1994.

1993

Vaiman, D., Bahridarwich, I., Mercier, D., Yerle, M., Eggen, A., Leveziel, H., Guerin, G., Gellin, J., Cribiu, E.P. :

Mapping of New Bovine Microsatellites on Cattle Chromosome-15 with Somatic Cell Hybrids, Linkage Analysis, and Fluorescence Insitu Hybridization Mammalian Genome 4:676-679, 1993. Pubmed reference: 8281017.

Fries, R., Eggen, A., Womack, J.E. :

The Bovine Genome Map (Vol 4, Pg 405, 1993) Mammalian Genome 4:731, 1993.

Toldo, S.S., Fries, R., Steffen, P., Neibergs, H.L., Barendse, W., Womack, J.E., Hetzel, D.J.S., Stranzinger, G. :

Physically Mapped, Cosmid-Derived Microsatellite Markers as Anchor Loci on Bovine Chromosomes Mammalian Genome 4:720-727, 1993. Pubmed reference: 8111120.

Barendse, W., Armitage, S.M., Kirkpatrick, B.W., Moore, S.S., Georges, M., Womack, J.E., Hetzel, J. :

A Genetic Map of Index DNA Loci on Bovine Chromosome 21 Genomics 18:598-601, 1993. Pubmed reference: 8307569.

Fries, R., Eggen, A., Womack, J.E. :

The bovine gene map Mammalian Genome 4:405-428, 1993. Pubmed reference: 8104056.

Rajcan-Separovic, E., Sabour, M.P. :

Fluorescence in situ hybridization of bovine Alu-like sequences to bovine and ovine chromosomes. Genome 36:984-6, 1993. Pubmed reference: 8270208. DOI: 10.1139/g93-129.

1992

Gallagher, D.S., Womack, J.E. :

Chromosome conservation in the Bovidae. J Hered 83:287-98, 1992. Pubmed reference: 1401875. DOI: 10.1093/oxfordjournals.jhered.a111215.

1991

Dollin, A.E., Murray, J.D., Gillies, C.B. :

Synaptonemal Complex Analysis of Hybrid Cattle .3. Meiotic Pairing Mechanisms in F1 Brahman X Hereford Hybrids Genome 34:228-235, 1991. Pubmed reference: 2055448.

Hediger, R., Ansari, H.A., Stranzinger, G.F. :

Chromosome banding and gene localizations support extensive conservation of chromosome structure between cattle and sheep. Cytogenet Cell Genet 57:127-34, 1991. Pubmed reference: 1717202. DOI: 10.1159/000133131.

Hayes, H., Petit, E., Dutrillaux, B. :

Comparison of RBG-banded karyotypes of cattle, sheep, and goats. Cytogenet Cell Genet 57:51-5, 1991. Pubmed reference: 1855392. DOI: 10.1159/000133114.

Dollin, A.E., Murray, J.D., Gillies, C.B. :

Synaptonemal complex analysis of hybrid cattle. II. Bos indicus x Bos taurus F1 and backcross hybrids. Genome 34:220-7, 1991. Pubmed reference: 2055447. DOI: 10.1139/g91-035.

Hayes, H., Petit, E. :

Comparison of RBG-Banded Karyotypes of Cattle, Sheep and Goat. Genetics Selection Evolution 23:S144-S147, 1991.

Di Berardino, D., Lioi, M.B., Matassino, D. :

Sequential GTG- RBA Banding Pattern in Prometaphase Chromosomes of Cattle (Bos taurus L). Genetics Selection Evolution 23:273-279, 1991.

Di Berardino, D., Lioi, M.B., Matassino, D. :

Sequential QFQ- RBA-Banding Pattern in Prometaphase Chromosomes of Cattle (Bos- Taurus L). Genetics Selection Evolution 23:385-390, 1991.

1990

Tambasco, A.J. :

Karyotypic Study of a Canchim Cattle Herd Revista Brasileira de Genetica 13:283-292, 1990.

Chiriaeva, O.G., Efimov, A.M., Smaragdov, M.G., Finashin, S.A., Smirnov, A.F. :

[The heterochromatin regions of the mitotic chromosomes in cattle]. Tsitologiia 32:626-32, 1990. Pubmed reference: 1700522.

Iannuzzi, L. :

An improved characterization of cattle chromosomes by means of high-resolution G- and R-band comparison. J Hered 81:80-3, 1990. Pubmed reference: 2332616. DOI: 10.1093/oxfordjournals.jhered.a110933.

DiBerardina, D., Hayes, H., Fries, R., Long, S. :

International system for cytogenetic nomenclature of domestic animals. The Second International Conference on Standardization of Domestic Animal Karyotypes, INRA, Jouy-en Josas, France, 22nd-26th May, 1989. Cytogenet Cell Genet 53:65-79, 1990. Pubmed reference: 11545113. DOI: 10.1159/000132898.

Iannuzzi, L., Dimeo, G.P., Perucatti, A., Ferrara, L. :

A Comparison of G-Banding and R-Banding in Cattle and River Buffalo Prometaphase Chromosomes. Caryologia 43:283-290, 1990.

Dimeo, G.P., Iannuzzi, L., Perucatti, A., Ferrara, L. :

Chromosome Markers in Cattle Revealed by High Resolution G+c- Bands. Caryologia 43:149-156, 1990.

1989

Fries, R., Beckmann, J.S., Georges, M., Soller, M., Womack, J. :

The bovine gene map. Anim Genet 20:3-29, 1989. Pubmed reference: 2567135. DOI: 10.1111/j.1365-2052.1989.tb00838.x.

Dollin, A.E., Murray, J.D., Gillies, C.B. :

Synaptonemal complex analysis of hybrid cattle. I. Pachytene substaging and the normal full bloods. Genome 32:856-64, 1989. Pubmed reference: 2620818. DOI: 10.1139/g89-522.

Chiryaeva, O.G., Amosova, A.V., Efimov, A.M., Smirnov, A.F., Kaminir, L.B., Yakovlev, A.F., Zelenin, A.V. :

Cytogenetic Mapping of Cattle (Bos-Taurus L) Using Quantitative Analysis of the Rba Map of Prometaphase Chromosomes. Cytogenetics of Animals, (ed. Halnan, C.R.E.) :211-219, 1989.

Halnan, C.R.E. :

Karyotype and Phenotype in Cattle and Hybrids of the Genus. Cytogenetics of Animals, (ed. Halnan, C.R.E.) :235-255, 1989.

Kopp, E. :

The Karyotype of the Permanent Bovine Cell Line Mdbk. Wiener Tierarztliche Monatsschrift 76:317-319, 1989.

1988

Bongso, T.A., Hilmi, M., Sopian, M., Zulkifli, S. :

Chromosomes of gaur cross domestic cattle hybrids. Res Vet Sci 44:251-4, 1988. Pubmed reference: 3387680.

Coates, J.W., Schmutz, S.M., Rousseaux, C.G. :

A survey of malformed aborted bovine fetuses, stillbirths and nonviable neonates for abnormal karyotypes. Can J Vet Res 52:258-63, 1988. Pubmed reference: 3370561.

Hondt, H.A. de, El-Nahass, E., Fathy, K. :

Cytogenetic studies on Egyptian native cattle and some of its crossbreds. Journal of Animal Breeding and Genetics 105:400-408, 1988.

Iwasaki, S., Shioya, Y., Hanada, A., Nakahara, T. :

Chromosomal preparation from 2-cell bovine embryos derived from follicular oocytes fertilized in vitro. Japanese Journal of Animal Reproduction 34:79-83, 1988.

Kiseleva, T.Yu. :

[Identification of nucleolus organizer regions on cattle chromosomes]. Byulleten' Vsesoyuznyi Nauchno- Issledovatel'skii Institut Razvedeniya i Genetiki Sel'skokhozyaistvennykh Zhivotnykh :17-20, 1988.

1987

Mayr, B., Gruber, K. :

Nucleolus organizer regions and heterochromatin in the zebu (Bos indicus L) Theoretical and Applied Genetics 73:832-835, 1987. Pubmed reference: 24241292.

Stranzinger, G., Elminger, B., Hetzel, D.J.S. :

Cytogenetic studies on different cattle breeds in Australia Journal of Animal Breeding and Genetics 104:231-234, 1987.

Grafodatskiĭ, A.S., Biltueva, L.S. :

[Homology of G-banded mammalian chromosomes]. Genetika 23:93-103, 1987. Pubmed reference: 3469125.

Namikawa, T., Amano, T., Okada, I., Hasnath, M.A., Haque, A.K.F., Majid, M.A. :

1986

Strel'chenko, N.S., Salerno, A., Andreeva, L.V., Mashurov, A.M., Sukhova, N.O., Deeva, V.S. :

[The karyotype of black-eared cattle at the 'Gutovskii' state farm in Novosibirsk region]. Sibirskii Vestnik Sel'skokhozaistvennoi Nauki :60-63, 1986.

1985

Chuanchai, V., Luesakul, C. :

[A study of normal karyotype in Thai native cattle and buffaloes]. Thai Journal of Veterinary Medicine 15:67-85, 1985.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

Proceedings of the First International Conference for the Standardisation of Banded Karyotypes of Domestic Animals. University of Reading Reading, England. 2nd-6th August 1976. Hereditas 92:145-62, 1980. Pubmed reference: 6103884. DOI: 10.1111/j.1601-5223.1980.tb01688.x.

1979

Bosma, A.A., Kroneman, J. :

Chromosome studies in cattle with hereditary zinc deficiency (lethal trait A 46) Veterinary Quarterly 1:121-125, 1979. Pubmed reference: 22039768.

Potter, W.L., Upton, P.C., Cooper, J., Blackshaw, A.W. :

C- and G-banding patterns and chromosomal morphology of some breeds of Australian cattle. Aust Vet J 55:560-7, 1979. Pubmed reference: 94258. DOI: 10.1111/j.1751-0813.1979.tb07046.x.

1978

Logue, D.N. :

Chromosome banding studies in cattle. Res Vet Sci 25:1-6, 1978. Pubmed reference: 705033.

1976

Gustavsson, I., Hageltorn, M., Zech, L. :

Recognition of the cattle chromosomes by the Q- and G-banding techniques. Hereditas 82:157-66, 1976. Pubmed reference: 59716. DOI: 10.1111/j.1601-5223.1976.tb01552.x.

1973

Hansen, K.M. :

Q-band karyotype of the goat (Capra hircus) and the relation between goat and bovine Q-bands. Hereditas 75:119-29, 1973. Pubmed reference: 4130421. DOI: 10.1111/j.1601-5223.1973.tb01148.x.

1971

Herzog, A., Hohn, H. :

Chromosome defects in hereditary parakeratosis of Black Pied calves. Giessener Beitrage zur Erbpathologie und Zuchthygiene 3:1-6, 1971.

1968

Kieffer, N.M., Cartwright, T.C. :

Sex chromosome polymorphism in domestic cattle. J Hered 59:34-6, 1968. Pubmed reference: 5656913.

1967

Basrur, P.K., Moon, Y.S. :

Chromosomes of cattle, bison, and their hybrid, the cattalo. Am J Vet Res 28:1319-25, 1967. Pubmed reference: 6053538.

Kieffer, N.M., Cartwright, T.C. :

Y chromosomes of Bos indicus and Bos taurus. Journal of Animal Science 26:204-205, 1967.

1964

Yosida, T.H., Lamontain, E.J. :

Chromosomes of normal and dwarf cattle Japanese Journal of Genetics 38:351-355, 1964.

BASRUR, P.K., GILMAN, J.P. :

BLOOD CULTURE METHOD FOR THE STUDY OF BOVINE CHROMOSOMES. Nature 204:1335-7, 1964. Pubmed reference: 14254442. DOI: 10.1038/2041335a0.

Jurmanova, K., Cerny, L. :

Somatic chromosomes in cattle. Sbornik Vysoke Skoly Zemedelske Brne, Series B 12:311-313, 1964.

1962

SASAKI, M.S., MAKINO, S. :

Revised study of the chromosomes of domestic cattle and the horse in somatic cells in vitro. J Hered 53:157-62, 1962. Pubmed reference: 13986625. DOI: 10.1093/oxfordjournals.jhered.a107156.

Bos taurus x Bison bison (beefalo) :

1967

Basrur, P.K., Moon, Y.S. :

Chromosomes of cattle, bison, and their hybrid, the cattalo. Am J Vet Res 28:1319-25, 1967. Pubmed reference: 6053538.

Bovichtus diacanthus :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Bovichtus variegatus (thornfish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Brachyistius frenatus (kelp perch) :

2023

Toy, J.A., Bernardi, G. :

A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. J Hered 114:404-409, 2023. Pubmed reference: 36790952. DOI: 10.1093/jhered/esad009.

Brachyteles arachnoides (woolly spider monkey) :

2025

Faulk, C., Walls, C., Nelson, B., Arakaki, P.R., Gonzalez, I.H.L., Banevicius, N., Teixeira, R.H.F., Medeiros, M.A., Silva, G.P., Talebi, M., Chung, W.C.J., Takeshita, R.S.C. :

De novo whole genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides). G3 (Bethesda) 15:jkaf034, 2025. Pubmed reference: 39960481. DOI: 10.1093/g3journal/jkaf034.

Brachyteles hypoxanthus :

2025

de Melo-Ximenes, A.A., Batista, R., Corvalán, L.C.J., Marques-Bonet, T., Kuderna, L., Farh, K., Rogers, J., Kaizer, M.D.C., Boubli, J.P., de Melo, F.R., Nunes, R., Telles, M.P.C. :

First assembly of a draft genome of the critically endangered Northern muriqui (Brachyteles hypoxanthus, Primates, Atelidae) including non-invasive genotyping strategies for the species. Ecol Evol 15:e71356, 2025. Pubmed reference: 40843033. DOI: 10.1002/ece3.71356.

Bradypodion pumilum :

2023

Taft, J.M., Tolley, K.A., Alexander, G.J., Geneva, A.J. :

De novo-whole genome assemblies for two Southern African dwarf chameleons (Bradypodion, Chamaeleonidae). Genome Biol Evol 15:evad182, 2023. Pubmed reference: 37847614. DOI: 10.1093/gbe/evad182.

Bradypodion ventrale (Southern dwarf chameleon) :

2023

Taft, J.M., Tolley, K.A., Alexander, G.J., Geneva, A.J. :

De novo-whole genome assemblies for two Southern African dwarf chameleons (Bradypodion, Chamaeleonidae). Genome Biol Evol 15:evad182, 2023. Pubmed reference: 37847614. DOI: 10.1093/gbe/evad182.

Bubalus bubalis (water buffalo) :

2025

Kumari, N., Kumar, S., Roy, A., Saini, P., Jaiswal, S., Iquebal, M.A., Angadi, U.B., Kumar, D. :

BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis. Database (Oxford) 2025:baae128, 2025. Pubmed reference: 39854213. DOI: 10.1093/database/baae128.

Pistucci, R., Cascone, I., Iannuzzi, A., Albarella, S., Kowal-Mierzwa, W., Zannotti, M., Iannuzzi, L., Parma, P. :

Comparative analysis of cattle (Bos taurus, 2n = 60) and river buffalo (Bubalus bubalis, 2n = 50) genome assemblies reveals two evolutionary conserved inversions and invalid centromere-telomere orientation of some autosomes. Anim Genet 56:e70031, 2025. Pubmed reference: 40721267. DOI: 10.1111/age.70031.

Arshad, F., Jayaraman, S., Talenti, A., Owen, R., Mohsin, M., Mansoor, S., Asif, M., Prendergast, J. :

A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection. Gigascience 14:giaf099, 2025. Pubmed reference: 40884803. DOI: 10.1093/gigascience/giaf099.

Di Maggio, F., Nunziato, M., Toscano, E., Sepe, L., Cimmino, R., Capolongo, E.A., Vasco, A., Paolella, G., Salvatore, F. :

A strategy for single-run sequencing of the water buffalo genome: (I) the use of third-generation technology to quickly produce long, high-quality reads. Animals (Basel) 15:2991, 2025. Pubmed reference: 41153918. DOI: 10.3390/ani15202991.

Toscano, E., Sepe, L., Di Maggio, F., Nunziato, M., Boccia, A., Cimmino, E., Scialla, A., Salvatore, F., Paolella, G. :

A strategy for single-run sequencing of the water buffalo genome: (II) Fast one-step assembly of highly continuous chromosome sequences. Animals (Basel) 15:3014, 2025. Pubmed reference: 41153941. DOI: 10.3390/ani15203014.

2024

Pineda, P.S., Flores, E.B., Villamor, L.P., Parac, C.J.M., Khatkar, M.S., Thu, H.T., Smith, T.P.L., Rosen, B.D., Ajmone-Marsan, P., Colli, L., Williams, J.L., Low, W.Y. :

Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project. Gigascience 13:giae053, 2024. Pubmed reference: 39250077. DOI: 10.1093/gigascience/giae053.

Shen, Y., An, Z., Xia, S., Ding, Q., Chen, K., Miao, Y., Wang, T., Zhong, J., Li, J., Wang, X., Wang, H. :

A multi-omics database of buffaloes from Yangtze valley reveals diversity of water buffalo (Bubalus bubalis). Sci Data 11:1375, 2024. Pubmed reference: 39695240. DOI: 10.1038/s41597-024-04246-4.

2023

Si, J., Dai, D., Li, K., Fang, L., Zhang, Y. :

A multi-tissue gene expression atlas of water buffalo (Bubalus bubalis) reveals transcriptome conservation between buffalo and cattle. Genes (Basel) 14:890, 2023. Pubmed reference: 37107649. DOI: 10.3390/genes14040890.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Ahmad, S.F., Chandrababu Shailaja, C., Vaishnav, S., Kumar, A., Gaur, G.K., Janga, S.C., Ahmad, S.M., Malla, W.A., Dutt, T. :

Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds. BMC Genomics 24:616, 2023. Pubmed reference: 37845620. DOI: 10.1186/s12864-023-09720-8.

2022

Khan, A., Singh, K., Jaiswal, S., Raza, M., Jasrotia, R.S., Kumar, A., Gurjar, A.K.S., Kumari, J., Nayan, V., Iquebal, M.A., Angadi, U.B., Rai, A., Datta, T.K., Kumar, D. :

Whole-genome-based web genomic resource for water buffalo (Bubalus bubalis). Front Genet 13:809741, 2022. Pubmed reference: 35480326. DOI: 10.3389/fgene.2022.809741.

Wang, X., Li, Z., Feng, T., Luo, X., Xue, L., Mao, C., Cui, K., Li, H., Huang, J., Huang, K., Rehman, S.U., Shi, D., Wu, D., Ruan, J., Liu, Q. :

Chromosome-level genome and recombination map of the male buffalo. Gigascience 12:giad063, 2022. Pubmed reference: 37589307. DOI: 10.1093/gigascience/giad063.

2021

Nascimento, A.V., Romero, A.R.S., Nawaz, M.Y., Cardoso, D.F., Santos, D.J.A., Gondro, C., Tonhati, H. :

An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly. Anim Genet 52:505-8, 2021. Pubmed reference: 34106478. DOI: 10.1111/age.13103.

2020

El-Khishin, D.A., Ageez, A., Saad, M.E., Ibrahim, A., Shokrof, M., Hassan, L.R., Abouelhoda, M.I. :

Sequencing and assembly of the Egyptian buffalo genome. PLoS One 15:e0237087, 2020. Pubmed reference: 32813723. DOI: 10.1371/journal.pone.0237087.

2019

Low, W.Y., Tearle, R., Bickhart, D.M., Rosen, B.D., Kingan, S.B., Swale, T., Thibaud-Nissen, F., Murphy, T.D., Young, R., Lefevre, L., Hume, D.A., Collins, A., Ajmone-Marsan, P., Smith, T.P.L., Williams, J.L. :

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun 10:260, 2019. Pubmed reference: 30651564. DOI: 10.1038/s41467-018-08260-0.

2017

Iamartino, D., Nicolazzi, E.L., Van Tassell, C.P., Reecy, J.M., Fritz-Waters, E.R., Koltes, J.E., Biffani, S., Sonstegard, T.S., Schroeder, S.G., Ajmone-Marsan, P., Negrini, R., Pasquariello, R., Ramelli, P., Coletta, A., Garcia, J.F., Ali, A., Ramunno, L., Cosenza, G., de Oliveira, D.A.A., Drummond, M.G., Bastianetto, E., Davassi, A., Pirani, A., Brew, F., Williams, J.L. :

Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis). PLoS One 12:e0185220, 2017. Pubmed reference: 28981529. DOI: 10.1371/journal.pone.0185220.

Williams, J.L., Iamartino, D., Pruitt, K.D., Sonstegard, T., Smith, T.P.L., Low, W.Y., Biagini, T., Bomba, L., Capomaccio, S., Castiglioni, B., Coletta, A., Corrado, F., Ferré, F., Iannuzzi, L., Lawley, C., Macciotta, N., McClure, M., Mancini, G., Matassino, D., Mazza, R., Milanesi, M., Moioli, B., Morandi, N., Ramunno, L., Peretti, V., Pilla, F., Ramelli, P., Schroeder, S., Strozzi, F., Thibaud-Nissen, F., Zicarelli, L., Ajmone-Marsan, P., Valentini, A., Chillemi, G., Zimin, A. :

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50). Gigascience 6:1-6, 2017. Pubmed reference: 29048578. DOI: 10.1093/gigascience/gix088.

1998

Iannuzzi, L. :

A genetic physical map in river buffalo (Bubalus bubalis, 2n=50) Caryologia 51:311-318, 1998.

1997

Dehondt, H.A., Gallagher, D., Oraby, H., Othman, O.E., Bosma, A.A., Womack, J.E., Elnahas, S.M. :

Gene mapping in the river buffalo (Bubalus bubalis l) - five syntenic groups Journal of Animal Breeding & Genetics-Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 114:79-85, 1997.

Yadav, B.R., Katiyar, P.K., Chauhan, M.S., Madan, M.L. :

Chromosome configuration during in vitro maturation of goat, sheep and buffalo oocytes. Theriogenology 47:943-51, 1997. Pubmed reference: 16728044. DOI: 10.1016/s0093-691x(97)00050-2.

Joshi, S.K., Govindaiah, M.G. :

Karyological studies in south kanara buffaloes of karnataka. Indian Veterinary Journal 74:1037-1039, 1997.

1996

Iannuzzi, L., Gallagher, D.S., Womack, J.E., Meo, G.P., Shelling, C.P., Groenen, M.A. :

1995

Iannuzzi, L., Di Meo, G.P. :

Guiraaraes, S.E., Pinheiro, L.E., Guimaraes, J.D. :

Meiotic peculiarities in hybrid buffalo. Theriogenology 43:579-83, 1995. Pubmed reference: 16727649. DOI: 10.1016/0093-691x(94)00063-z.

Dimeo, G.P., Perucatti, A., Iannuzzi, L., Rangelfigueiredo, M.T., Ferrara, L. :

Constitutive heterochromatin polymorphism in river buffalo chromosomes. Caryologia 48:137-146, 1995.

1994

Iannuzzi, L. :

Standard karyotype of the river buffalo (Bubalus bubalis L., 2n = 50). Report of the committee for the standardization of banded karyotypes of the river buffalo. Cytogenet Cell Genet 67:102-13, 1994. Pubmed reference: 8039419. DOI: 10.1159/000133808.

Ramesha, K.P., Goswami, S.L. :

Chromosome analysis of Murrah buffalo (Bubalus bubalis ) spermatozoa using zona-free hamster oocytes. Theriogenology 42:297-305, 1994. Pubmed reference: 16727537. DOI: 10.1016/0093-691x(94)90274-7.

1992

Hishinuma, M., Hilmi, M., Takahashi, Y., Mori, Y., Kanai, Y., Jainudeen, M.R., Kanagawa, H. :

High-resolution GTG-banding of chromosomes in the swamp buffalo (Bubalus bubalis L.): description of chromosome 1. Hereditas 117:97-101, 1992. Pubmed reference: 1399708. DOI: 10.1111/j.1601-5223.1992.tb00013.x.

Ramesha, K.P., Hegde, B.P. :

Chromosomes of Surti and Non- Descript Buffaloes of Karnataka. Indian Veterinary Journal 69:34-37, 1992.

1990

Iannuzzi, L., Di Meo, G.P., Perucatti, A., Ferrara, L. :

The high resolution G- and R-banding pattern in chromosomes of river buffalo (Bubalus bubalis L.). Hereditas 112:209-15, 1990. Pubmed reference: 2211179. DOI: 10.1111/j.1601-5223.1990.tb00059.x.

Iannuzzi, L., Dimeo, G.P., Perucatti, A., Ferrara, L. :

A Comparison of G-Banding and R-Banding in Cattle and River Buffalo Prometaphase Chromosomes. Caryologia 43:283-290, 1990.

1989

Harisah, M., Azmi, T.I., Hilmi, M., Vidyadaran, M.K., Bongso, T.A., Nava, Z.M., Momongan, V., Basrur, P.K. :

Identification of crossbred buffalo genotypes and their chromosome segregation patterns. Genome 32:999-1002, 1989. Pubmed reference: 2628159. DOI: 10.1139/g89-544.

1987

Amano, T., Namikawa, T., Okada, I., Hasnath, M.A., Faruque, M.O., Majid, M.A. :

Karyotypes and blood protein polymorphisms of native water buffaloes in Bangladesh. Genetic studies on breed differentiation of the native domestic animals in Bangladesh. Faculty of Applied Biological Science, Hiroshima University, Hiroshima :117-128, 1987.

Huang, Y.J., Xie, M.O., Liu, Y.J., Tan, Z.S. :

[Observations on G- and C-banding karyotypes in water buffaloes]. Hereditas, China 9:13-16, 1987.

1986

Bidahr, G.C., Pattnaik, G.R., Rao, P.K., Patro, B.N. :

Chromosome number and morphology of Paralakhemundi buffaloes in Orissa. Buffalo Bulletin 5:54-56, 1986.

Jorge, W., Rocha, G., Villares, J.B. :

[Morphology of the Y chromosome in the buffalo]. Revista da Sociedade Brasileira de Zootecnia 15:142-144, 1986.

1985

Chuanchai, V., Luesakul, C. :

[A study of normal karyotype in Thai native cattle and buffaloes]. Thai Journal of Veterinary Medicine 15:67-85, 1985.

1984

Livescu, B.E., Granciu, I., Draganescu, C. :

[Some considerations concerning the evolution of the karyotype in buffaloes]. Lucrari stiintifice, Institutul de Cercetare si Productie pentru Cresterea Bovinelor :41-50, 1984.

1983

Bongso, T.A., Hilmi, M., Basrur, P.K. :

Testicular cells in hybrid water buffaloes (Bubalus bubalis). Res Vet Sci 35:253-8, 1983. Pubmed reference: 6665308.

Bucorvus leadbeateri (southern ground hornbill) :

2025

Patel, J., Botes, A., Mollett, J., De Maayer, P. :

Whole genome sequencing, assembly and annotation of the Southern Ground Hornbill - Bucorvus leadbeateri. Sci Data 12:58, 2025. Pubmed reference: 39799121. DOI: 10.1038/s41597-025-04412-2.

Budorcas taxicolor (takin) :

1994

Pasitschniak-Arts, M., Flood, P.F., Schmutz, S.M., Seidel, B. :

A comparison of G-band patterns of the muskox and takin and their evolutionary relationship to sheep. J Hered 85:143-7, 1994. Pubmed reference: 8182282. DOI: 10.1093/oxfordjournals.jhered.a111415.

Bufotes viridis (European green toad) :

2025

Rödin-Mörch, P., Bunikis, I., Choi, E., Ciofi, C., Diedericks, G., Diroma, M.A., Einarsdóttir, E., Försäter, K., Heintz, J., Jonsäll, L., Lantz, H., Laurila, A., Leitão, H.G., Mosbech, M.B., Natali, C., Olsen, R.A., Vinnere Pettersson, O., Soler, L., Svardal, H., Proux-Wéra, E., Höglund, J. :

A chromosome-level genome assembly of the European green toad (Bufotes viridis). G3 (Bethesda) 15:jkaf002, 2025. Pubmed reference: 39969399. DOI: 10.1093/g3journal/jkaf002.

Bungarus multicinctus (many-banded krait) :

2023

Liu, B., Cui, L., Deng, Z., Ma, Y., Yang, D., Gong, Y., Xu, Y., Lan, T., Yang, S., Huang, S. :

The genome assembly and annotation of the many-banded krait, Bungarus multicinctus. GigaByte 2023:gigabyte82, 2023. Pubmed reference: 37404266. DOI: 10.46471/gigabyte.82.

Cacatua galerita (sulfur-crested cockatoo) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Cairina moschata (Muscovy duck) :

2021

Jiang, F., Jiang, Y., Wang, W., Xiao, C., Lin, R., Xie, T., Sung, W.K., Li, S., Jakovlić, I., Chen, J., Du, X. :

A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. BMC Genomics 22:581, 2021. Pubmed reference: 34330207. DOI: 10.1186/s12864-021-07897-4.

1997

Denjean, B., Ducos, A., Darre, A., Pinton, A., Seguela, A., Berland, H., Blanc, M.F., Fillon, V., Darre, R. :

Karyotypes of mallard (anas platyrhynchos) and muscovy (cairina moschata) ducks, and of their hybrid [French]. Revue de Medecine Veterinaire 148:695-704, 1997.

1986

Migliore, L., Tesoro, M., Romboli, I. :

Chromosome complement and C-banding pattern in the Muscovy duck (Cairina moschata domestica L). 7th European Poultry Conference, Paris 1986. World's Poultry Science association, Paris 1:99-103, 1986.

Callipepla californica (California quail) :

2023

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., Bowie, R.C.K. :

A highly contiguous genome assembly for the California quail (Callipepla californica). J Hered 114:418-427, 2023. Pubmed reference: 36763048. DOI: 10.1093/jhered/esad008.

Callithrix jacchus (white-tufted-ear marmoset) :

2023

Harris, R.A., Raveendran, M., Warren, W., LaDeana, H.W., Tomlinson, C., Graves-Lindsay, T., Green, R.E., Schmidt, J.K., Colwell, J.C., Makulec, A.T., Cole, S.A., Cheeseman, I.H., Ross, C.N., Capuano, S., Eichler, E.E., Levine, J.E., Rogers, J. :

Whole genome analysis of SNV and Indel polymorphism in common marmosets (Callithrix jacchus). Genes (Basel) 14:2185, 2023. Pubmed reference: 38137007. DOI: 10.3390/genes14122185.

2021

Yang, C., Zhou, Y., Marcus, S., Formenti, G., Bergeron, L.A., Song, Z., Bi, X., Bergman, J., Rousselle, M.M.C., Zhou, C., Zhou, L., Deng, Y., Fang, M., Xie, D., Zhu, Y., Tan, S., Mountcastle, J., Haase, B., Balacco, J., Wood, J., Chow, W., Rhie, A., Pippel, M., Fabiszak, M.M., Koren, S., Fedrigo, O., Freiwald, W.A., Howe, K., Yang, H., Phillippy, A.M., Schierup, M.H., Jarvis, E.D., Zhang, G. :

Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature 594(7862):227-233, 2021. Pubmed reference: 33910227. DOI: 10.1038/s41586-021-03535-x.

2020

Jayakumar, V., Ishii, H., Seki, M., Kumita, W., Inoue, T., Hase, S., Sato, K., Okano, H., Sasaki, E., Sakakibara, Y. :

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data. BMC Genomics 21:243, 2020. Pubmed reference: 32241258. DOI: 10.1186/s12864-020-6657-2.

1996

Sherlock, J.K., Griffin, D.K., Delhanty, J.D., Parrington, J.M. :

Homologies between human and marmoset (Callithrix jacchus) chromosomes revealed by comparative chromosome painting. Genomics 33:214-9, 1996. Pubmed reference: 8660970. DOI: 10.1006/geno.1996.0186.

Caloenas nicobarica (Nicobar pigeon) :

2025

Alexandre, N., Balacco, J., Tilley, T., Abueg, L., Brajuka, N., Moreira, L.R., Whelan, C., Schwarz Taylor, E., Jarvis, E.D., Fedrigo, O., Shapiro, B., Keyte, A.L. :

A Chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica. J Hered :esaf031, 2025. Pubmed reference: 40371976. DOI: 10.1093/jhered/esaf031.

Calotes versicolor (garden lizard) :

2023

Wang, Q., He, F., Huang, R.Y., Yang, X., Yang, D., Ngatia, J.N., Gong, Y., Xu, Y., Huang, S., Liu, H. :

Draft genome of the oriental garden lizard (Calotes versicolor). Front Genet 14:1091544, 2023. Pubmed reference: 36891152. DOI: 10.3389/fgene.2023.1091544.

Calotriton arnoldi (Montseny brook newt) :

2024

Talavera, A., Palmada-Flores, M., Burriel-Carranza, B., Valbuena-Ureña, E., Mochales-Riaño, G., Adams, D.C., Tejero-Cicuéndez, H., Soler-Membrives, A., Amat, F., Guinart, D., Carbonell, F., Obon, E., Marquès-Bonet, T., Carranza, S. :

Genomic insights into the Montseny brook newt (Calotriton arnoldi), a critically endangered glacial relict. iScience 27:108665, 2024. Pubmed reference: 38226169. DOI: 10.1016/j.isci.2023.108665.

Calotriton asper (Pyrenean brook newt) :

2024

Calypte anna (Anna's hummingbird) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Camelus bactrianus (Bactrian camel) :

2025

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

Vijh, R.K., Sharma, U., Arora, R., Kapoor, P., Raheja, M., Sharma, R., Ahlawat, S., Dureja, V. :

Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids. Gene 921:148541, 2024. Pubmed reference: 38723784. DOI: 10.1016/j.gene.2024.148541.

Guo, L., Dao, L., Liu, B., Wang, J., Liu, Z., Ma, F., Morigen, B., Chang, C., Bai, Y., Guo, Y., Shi, C., Cao, J., Zhang, W. :

Development and application of a 1K functional liquid chip for lactation performance in Bactrian camels. Front Vet Sci 11:1359923, 2024. Pubmed reference: 39021409. DOI: 10.3389/fvets.2024.1359923.

2023

Bei, L., He, C., Liu, J., Han, C., Zhou, H. :

Genome-wide identification and characterization of microsatellite markers in Bactrian Camel. Genomics 115:110726, 2023. Pubmed reference: 37832857. DOI: 10.1016/j.ygeno.2023.110726.

2019

Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :

Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

Camelus dromedarius (Arabian camel) :

2024

Vijh, R.K., Sharma, U., Arora, R., Kapoor, P., Raheja, M., Sharma, R., Ahlawat, S., Dureja, V. :

Bahbahani, H., Mohammad, Z., Al-Ateeqi, A., Almathen, F. :

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data. Sci Rep 14:25573, 2024. Pubmed reference: 39462079. DOI: 10.1038/s41598-024-77773-0.

2020

Sabahat, S., Brauning, R., Clarke, S.M., Nadeem, A., Thomson, P.C., Khatkar, M.S. :

SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method. Anim Genet 51:620-623, 2020. Pubmed reference: 32421863. DOI: 10.1111/age.12953.

2019

Ruvinskiy, D., Larkin, D.M., Farré, M. :

A near chromosome assembly of the dromedary camel genome. Front Genet 10:32, 2019. Pubmed reference: 30804979. DOI: 10.3389/fgene.2019.00032.

Futas, J., Oppelt, J., Jelinek, A., Elbers, J.P., Wijacki, J., Knoll, A., Burger, P.A., Horin, P. :

Natural killer cell receptor genes in camels: Another mammalian model. Front Genet 10:620, 2019. Pubmed reference: 31312212. DOI: 10.3389/fgene.2019.00620.

1992

Samman, M.A., Alsaleh, A.A., Sheth, K.V. :

Detailed Description and Nomenclature of G-Banded Arabian Camel (Camelus dromedarius) Chromosomes. Caryologia 45:359-365, 1992.

Campylomormyrus compressirostris :

2023

Cheng, F., Dennis, A.B., Osuoha, J.I., Canitz, J., Kirschbaum, F., Tiedemann, R. :

A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC Genomics 24:129, 2023. Pubmed reference: 36941548. DOI: 10.1186/s12864-023-09196-6.

Canis aureus (golden jackal) :

2023

Sosale, M.S., Songsasen, N., İbiş, O., Edwards, C.W., Figueiró, H.V., Koepfli, K.P. :

The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica). Gene 866:147303, 2023. Pubmed reference: 36854348. DOI: 10.1016/j.gene.2023.147303.

Canis latrans (coyote) :

2024

Bredemeyer, K.R., vonHoldt, B.M., Foley, N.M., Childers, I., Brzeski, K.E., Murphy, W.J. :

The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies. J Hered 115:480-486, 2024. Pubmed reference: 38416051. DOI: 10.1093/jhered/esae013.

Canis lupus (gray wolf) :

2025

Hervey, S.D., vonHoldt, B.M., Romanski, M.C., Wheeldon, T.J., Patterson, B.R., Brzeski, K.E. :

Development of a noninvasive genotyping-in-thousands (GTseq) panel for long-term conservation of Western Great Lakes gray wolves (Canis lupus). Ecol Evol 15:e71240, 2025. Pubmed reference: 40260146. DOI: 10.1002/ece3.71240.

2024

Smeds, L., Huson, L.S.A., Ellegren, H. :

Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 17:e13652, 2024. Pubmed reference: 38333557. DOI: 10.1111/eva.13652.

Bredemeyer, K.R., vonHoldt, B.M., Foley, N.M., Childers, I., Brzeski, K.E., Murphy, W.J. :

2019

Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., Zhai, S., Xiao, J., Zhang, Z., Bao, Y., Zhang, Y.P., Wang, G.D., Zhao, W. :

iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 47:D793-D800, 2019. Pubmed reference: 30371881. DOI: 10.1093/nar/gky1041.

Canis lupus dingo (dingo) :

2023

Ballard, J.W.O., Field, M.A., Edwards, R.J., Wilson, L.A.B., Koungoulos, L.G., Rosen, B.D., Chernoff, B., Dudchenko, O., Omer, A., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Chan, E., Zammit, R., Hayes, V., Aiden, E.L. :

The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 12:giad018, 2023. Pubmed reference: 36994871. DOI: 10.1093/gigascience/giad018.

Canis lupus familiaris (dog) :

2025

Nachiappan, R.K., Arora, R., Vijh, R.K., Sharma, U., Raheja, M., Sharma, M., Maggon, M., Ahlawat, S. :

Empowering canine genomics: Design and validation of a High-Density SNP array for Indian dogs. Genome 68:1-12, 2025. Pubmed reference: 39869854. DOI: 10.1139/gen-2024-0094.

[No authors listed] :

Correction to 'iDog: a multi-omics resource for canids study'. Nucleic Acids Res 53:gkaf194, 2025. Pubmed reference: 40052825. DOI: 10.1093/nar/gkaf194.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Rizzoli, E., Fievez, L., Fastrès, A., Roels, E., Marichal, T., Clercx, C. :

A single-cell RNA sequencing atlas of the healthy canine lung: a foundation for comparative studies. Front Immunol 16:1501603, 2025. Pubmed reference: 40114924. DOI: 10.3389/fimmu.2025.1501603.

Schall, P.Z., Kidd, J.M. :

Integrative genotyping and analysis of canine structural variation using long-read and short-read data. Genome Biol Evol 17:evaf173, 2025. Pubmed reference: 40971676. DOI: 10.1093/gbe/evaf173.

2024

Nguyen, A.K., Schall, P.Z., Kidd, J.M. :

A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 35:565-576, 2024. Pubmed reference: 39088040. DOI: 10.1007/s00335-024-10056-1.

Nguyen, A.K., Blacksmith, M.S., Kidd, J.M. :

Duplications and retrogenes are numerous and widespread in modern canine genomic assemblies. Genome Biol Evol 16:evae142, 2024. Pubmed reference: 38946312. DOI: 10.1093/gbe/evae142.

Bougiouri, K., Aninta, S.G., Charlton, S., Harris, A., Carmagnini, A., Piličiauskienė, G., Feuerborn, T.R., Scarsbrook, L., Tabadda, K., Blaževičius, P., Parker, H.G., Gopalakrishnan, S., Larson, G., Ostrander, E.A., Irving-Pease, E.K., Frantz, L.A.F., Racimo, F. :

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years. bioRxiv , 2024. Pubmed reference: 38903121. DOI: 10.1101/2024.03.15.585179.

Nebenführ, M., Prochotta, D., Ben Hamadou, A., Janke, A., Gerheim, C., Betz, C., Greve, C., Bolz, H.J. :

High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog's genome. GigaByte 2024:gigabyte134, 2024. Pubmed reference: 39314919. DOI: 10.46471/gigabyte.134.

Zhou, T., Pu, S.Y., Zhang, S.J., Zhou, Q.J., Zeng, M., Lu, J.S., Lu, X., Wang, Y.N., Wang, G.D. :

Dog10K: an integrated Dog10K database summarizing canine multi-omics. Nucleic Acids Res 53:D939-D947, 2024. Pubmed reference: 39436034. DOI: 10.1093/nar/gkae928.

Liu, Y., Wang, Y., Sun, J., Kong, D., Zhou, B., Ding, M., Meng, Y., Duan, G., Cui, Y., Fan, Z., Zhang, Y.P., Zhao, W., Tang, B. :

iDog: a multi-omics resource for canids study. Nucleic Acids Res 53:D1039-D1046, 2024. Pubmed reference: 39526388. DOI: 10.1093/nar/gkae1031.

Hörtenhuber, M., Hytönen, M.K., Mukarram, A.K., Arumilli, M., Araujo, C.L., Quintero, I., Syrjä, P., Airas, N., Kaukonen, M., Kyöstilä, K., Niskanen, J., Jokinen, T.S., Mottaghitalab, F., Takan, I., Salokorpi, N., Raman, A., Stevens, I., Iivanainen, A., Yoshihara, M., Gusev, O., Bannasch, D., Sukura, A., Schoenebeck, J.J. :

The DoGA consortium expression atlas of promoters and genes in 100 canine tissues. Nat Commun 15:9082, 2024. Pubmed reference: 39433728. DOI: 10.1038/s41467-024-52798-1.

Schall, P.Z., Meadows, J.R.S., Ramos-Almodovar, F., Kidd, J.M. :

Characterization of nuclear mitochondrial insertions in canine genome assemblies. Genes (Basel) 15:1318, 2024. Pubmed reference: 39457442. DOI: 10.3390/genes15101318.

2023

Hsu, W.T., Williamson, P., Khatkar, M.S. :

Identification of genomic signatures in Bullmastiff dogs using composite selection signals analysis of 23 purebred clades. Animals (Basel) 13:1149, 2023. Pubmed reference: 37048405. DOI: 10.3390/ani13071149.

Kowal, K., Tkaczyk-Wlizło, A., Jusiak, M., Grzybowska-Szatkowska, L., Ślaska, B. :

Canis MitoSNP database: a functional tool useful for comparative analyses of human and canine mitochondrial genomes. J Appl Genet 64:515-520, 2023. Pubmed reference: 37351774. DOI: 10.1007/s13353-023-00764-w.

Son, K.H., Aldonza, M.B.D., Nam, A.R., Lee, K.H., Lee, J.W., Shin, K.J., Kang, K., Cho, J.Y. :

Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. Sci Adv 9:eade3399, 2023. Pubmed reference: 37406108. DOI: 10.1126/sciadv.ade3399.

Duhan, N., Kaur, S., Kaundal, R. :

Meadows, J.R.S., Kidd, J.M., Wang, G.D., Parker, H.G., Schall, P.Z., Bianchi, M., Christmas, M.J., Bougiouri, K., Buckley, R.M., Hitte, C., Nguyen, A.K., Wang, C., Jagannathan, V., Niskanen, J.E., Frantz, L.A.F., Arumilli, M., Hundi, S., Lindblad-Toh, K., Ginja, C., Agustina, K.K., André, C., Boyko, A.R., Davis, B.W., Drögemüller, M., Feng, X.Y., Gkagkavouzis, K., Iliopoulos, G., Harris, A.C., Hytönen, M.K., Kalthoff, D.C., Liu, Y.H., Lymberakis, P., Poulakakis, N., Pires, A.E., Racimo, F., Ramos-Almodovar, F., Savolainen, P., Venetsani, S., Tammen, I., Triantafyllidis, A., vonHoldt, B., Wayne, R.K., Larson, G., Nicholas, F.W., Lohi, H., Leeb, T., Zhang, Y.P., Ostrander, E.A. :

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 24:187, 2023. Pubmed reference: 37582787. DOI: 10.1186/s13059-023-03023-7.

Schall, P.Z., Winkler, P.A., Petersen-Jones, S.M., Yuzbasiyan-Gurkan, V., Kidd, J.M. :

Genome-wide methylation patterns from canine nanopore assemblies. G3 (Bethesda) 13:jkad203, 2023. Pubmed reference: 37681359. DOI: 10.1093/g3journal/jkad203.

Du, W., Liu, X., Huang, L., Zheng, Y., Wu, W., Huang, Q., Li, T., Wei, R., Yang, Q., Deng, S., Liao, J., Liu, C., Chen, L. :

Developmental validation of a novel multiple genotyping assay with 24 canine STR loci. Vet Q 43:1-18, 2023. Pubmed reference: 37746714. DOI: 10.1080/01652176.2023.2262521.

Yang, I.S., Jang, I., Yang, J.O., Choi, J., Kim, M.S., Kim, K.K., Seung, B.J., Cheong, J.H., Sur, J.H., Nam, H., Lee, B., Kim, J., Kim, S. :

CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 24:613, 2023. Pubmed reference: 37828501. DOI: 10.1186/s12864-023-09655-0.

2021

Wang, C., Wallerman, O., Arendt, M.L., Sundström, E., Karlsson, Å., Nordin, J., Mäkeläinen, S., Pielberg, G.R., Hanson, J., Ohlsson, Å., Saellström, S., Rönnberg, H., Ljungvall, I., Häggström, J., Bergström, T.F., Hedhammar, Å., Meadows, J.R.S., Lindblad-Toh, K. :

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol 4:185, 2021. Pubmed reference: 33568770. DOI: 10.1038/s42003-021-01698-x.

Edwards, R.J., Field, M.A., Ferguson, J.M., Dudchenko, O., Keilwagen, J., Rosen, B.D., Johnson, G.S., Rice, E.S., Hillier, D., Hammond, J.M., Towarnicki, S.G., Omer, A., Khan, R., Skvortsova, K., Bogdanovic, O., Zammit, R.A., Aiden, E.L., Warren, W.C., Ballard, J.W.O. :

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22:188, 2021. Pubmed reference: 33726677. DOI: 10.1186/s12864-021-07493-6.

Jagannathan, V., Hitte, C., Kidd, J.M., Masterson, P., Murphy, T.D., Emery, S., Davis, B., Buckley, R.M., Liu, Y.H., Zhang, X.Q., Leeb, T., Zhang, Y.P., Ostrander, E.A., Wang, G.D. :

Dog10K_Boxer_Tasha_1.0: A long-read assembly of the dog reference genome. Genes (Basel) 12:847, 2021. Pubmed reference: 34070911. DOI: 10.3390/genes12060847.

Serres-Armero, A., Davis, B.W., Povolotskaya, I.S., Morcillo-Suarez, C., Plassais, J., Juan, D., Ostrander, E.A., Marques-Bonet, T. :

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 31:762-774, 2021. Pubmed reference: 33863806. DOI: 10.1101/gr.266049.120.

2020

Field, M.A., Rosen, B.D., Dudchenko, O., Chan, E.K.F., Minoche, A.E., Edwards, R.J., Barton, K., Lyons, R.J., Tuipulotu, D.E., Hayes, V.M., D Omer, A., Colaric, Z., Keilwagen, J., Skvortsova, K., Bogdanovic, O., Smith, M.A., Aiden, E.L., Smith, T.P.L., Zammit, R.A., Ballard, J.W.O. :

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 9:giaa027, 2020. Pubmed reference: 32236524. DOI: 10.1093/gigascience/giaa027.

2019

Hayward, J.J., White, M.E., Boyle, M., Shannon, L.M., Casal, M.L., Castelhano, M.G., Center, S.A., Meyers-Wallen, V.N., Simpson, K.W., Sutter, N.B., Todhunter, R.J., Boyko, A.R. :

Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genet 15:e1008003, 2019. Pubmed reference: 31525180. DOI: 10.1371/journal.pgen.1008003.

Ostrander, E.A., Wang, G.D., Larson, G., vonHoldt, B.M., Davis, B.W., Jagannathan, V., Hitte, C., Wayne, R.K., Zhang, Y.P. :

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health. Natl Sci Rev 6:810-824, 2019. Pubmed reference: 31598383. DOI: 10.1093/nsr/nwz049.

Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., Zhai, S., Xiao, J., Zhang, Z., Bao, Y., Zhang, Y.P., Wang, G.D., Zhao, W. :

iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 47:D793-D800, 2019. Pubmed reference: 30371881. DOI: 10.1093/nar/gky1041.

2018

Holden, L.A., Arumilli, M., Hytönen, M.K., Hundi, S., Salojärvi, J., Brown, K.H., Lohi, H. :

Assembly and analysis of unmapped genome sequence reads reveal novel sequence and variation in dogs. Sci Rep 8:10862, 2018. Pubmed reference: 30022108. DOI: 10.1038/s41598-018-29190-3.

2014

Hoeppner, M.P., Lundquist, A., Pirun, M., Meadows, J.R., Zamani, N., Johnson, J., Sundström, G., Cook, A., Fitzgerald, M.G., Swofford, R., Mauceli, E., Moghadam, B.T., Greka, A., Alföldi, J., Abouelleil, A., Aftuck, L., Bessette, D., Berlin, A., Brown, A., Gearin, G., Lui, A., Macdonald, J.P., Priest, M., Shea, T., Turner-Maier, J., Zimmer, A., Lander, E.S., di Palma, F., Lindblad-Toh, K., Grabherr, M.G. :

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One 9:e91172, 2014. Pubmed reference: 24625832. DOI: 10.1371/journal.pone.0091172.

2010

Wong, A.K., Ruhe, A.L., Dumont, B.L., Robertson, K.R., Guerrero, G., Shull, S.M., Ziegle, J.S., Millon, L.V., Broman, K.W., Payseur, B.A., Neff, M.W. :

A comprehensive linkage map of the dog genome. Genetics 184:595-605, 2010. Pubmed reference: 19966068. DOI: 10.1534/genetics.109.106831.

2008

Thomas, R., Duke, S.E., Karlsson, E.K., Evans, A., Ellis, P., Lindblad-Toh, K., Langford, C.F., Breen, M. :

A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenet Genome Res 122:110-21, 2008. Pubmed reference: 19096206. DOI: 10.1159/000163088.

2007

Thomas, R., Duke, S.E., Bloom, S.K., Breen, T.E., Young, A.C., Feiste, E., Seiser, E.L., Tsai, P.C., Langford, C.F., Ellis, P., Karlsson, E.K., Lindblad-Toh, K., Breen, M. :

A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered 98:474-84, 2007. Pubmed reference: 17702974. DOI: 10.1093/jhered/esm053.

Sargan, D.R., Aguirre-Hernandez, J., Galibert, F., Ostrander, E.A. :

An extended microsatellite set for linkage mapping in the domestic dog. J Hered 98:221-31, 2007. Pubmed reference: 17406025. DOI: 10.1093/jhered/esm006.

2005

Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J., Zody, M.C., Mauceli, E., Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., DeJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.W., Cook, A., Cuff, J., Daly, M.J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.P., Parker, H.G., Pollinger, J.P., Searle, S.M., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., DeGray, S., Dhargay, N., Dooley, K., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., FitzGerald, M., Foley, K., Foley, C., Franke, A., Friedrich, D., Gage, D., Garber, M., Gearin, G., Giannoukos, G., Goode, T., Goyette, A., Graham, J., Grandbois, E., Gyaltsen, K., Hafez, N., Hagopian, D., Hagos, B., Hall, J., Healy, C., Hegarty, R., Honan, T., Horn, A., Houde, N., Hughes, L., Hunnicutt, L., Husby, M., Jester, B., Jones, C., Kamat, A., Kanga, B., Kells, C., Khazanovich, D., Kieu, A.C., Kisner, P., Kumar, M., Lance, K., Landers, T., Lara, M., Lee, W., Leger, J.P., Lennon, N., Leuper, L., LeVine, S., Liu, J., Liu, X., Lokyitsang, Y., Lokyitsang, T., Lui, A., Macdonald, J., Major, J., Marabella, R., Maru, K., Matthews, C., McDonough, S., Mehta, T., Meldrim, J., Melnikov, A., Meneus, L., Mihalev, A., Mihova, T., Miller, K., Mittelman, R., Mlenga, V., Mulrain, L., Munson, G., Navidi, A., Naylor, J., Nguyen, T., Nguyen, N., Nguyen, C., Nguyen, T., Nicol, R., Norbu, N., Norbu, C., Novod, N., Nyima, T., Olandt, P., O'Neill, B., O'Neill, K., Osman, S., Oyono, L., Patti, C., Perrin, D., Phunkhang, P., Pierre, F., Priest, M., Rachupka, A., Raghuraman, S., Rameau, R., Ray, V., Raymond, C., Rege, F., Rise, C., Rogers, J., Rogov, P., Sahalie, J., Settipalli, S., Sharpe, T., Shea, T., Sheehan, M., Sherpa, N., Shi, J., Shih, D., Sloan, J., Smith, C., Sparrow, T., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Stone, S., Sykes, S., Tchuinga, P., Tenzing, P., Tesfaye, S., Thoulutsang, D., Thoulutsang, Y., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Venkataraman, V., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Yang, S., Yang, X., Young, G., Yu, Q., Zainoun, J., Zembek, L., Zimmer, A., Lander, E.S. :

Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-19, 2005. Pubmed reference: 16341006. DOI: 10.1038/nature04338.

2004

Switonski, M., Szczerbal, I., Nowacka, J. :

The dog genome map and its use in mammalian comparative genomics. J Appl Genet 45:195-214, 2004. Pubmed reference: 15131351.

2003

Guyon, R., Lorentzen, T.D., Hitte, C., Kim, L., Cadieu, E., Parker, H.G., Quignon, P., Lowe, J.K., Renier, C., Gelfenbeyn, B., Vignaux, F., DeFrance, H.B., Gloux, S., Mahairas, G.G., Andre, C., Galibert, F., Ostrander, E.A. :

A 1-Mb resolution radiation hybrid map of the canine genome Proceedings of the National Academy of Sciences of the United States of America 100:5296-301, 2003. Pubmed reference: 12700351. DOI: 10.1073/pnas.0831002100.

Spriggs, H.F., Holmes, N.G., Breen, M.G., Deloukas, P.G., Langford, C.F., Ross, M.T., Carter, N.P., Davis, M.E., Knights, C.E., Smith, A.E., Farr, C.J., McCarthy, L.C., Binns, M.M. :

Construction and integration of radiation-hybrid and cytogenetic maps of dog Chromosome X Mammalian Genome 14:214-21, 2003. Pubmed reference: 12647244. DOI: 10.1007/s00335-002-3051-0.

Roberts, M.C., Hitte, C.C., Hendrickson, J.A., Hoffmann, D.E., Flickinger, G.H., Rutherford, M.S., Guyon, R.S., Galibert, F.S., Mickelson, J.R. :

Characterization and radiation hybrid mapping of expressed sequence tags from the canine brain Mammalian Genome 14:203-13, 2003. Pubmed reference: 12647243. DOI: 10.1007/s00335-002-2207-2.

2002

Dukes-McEwan, J., Jackson, I.J. :

The promises and problems of linkage analysis by using the current canine genome map Mammalian Genome 13:667-672, 2002. Pubmed reference: 12461654. DOI: 10.1007/s00335-002-4004-3.

2001

Breen, M., Jouquand, S., Renier, C., Mellersh, C.S., Hitte, C., Holmes, N.G., Cheron, A., Suter, N., Vignaux, F., Bristow, A.E., Priat, C., McCann, E., Andre, C., Boundy, S., Gitsham, P., Thomas, R., Bridge, W.L., Spriggs, H.F., Ryder, E.J., Curson, A., Sampson, J., Ostrander, E.A., Binns, M.M., Galibert, F. :

Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes Genome Research 11:1784-1795, 2001. Pubmed reference: 11591656. DOI: 10.1101/gr.189401.

2000

Mellersh, C.S., Hitte, C., Richman, M., Vignaux, F., Priat, C., Jouquand, S., Werner, P., Andre, C., DeRose, S., Patterson, D.F., Ostrander, E.A., Galibert, F. :

An integrated linkage-radiation hybrid map of the canine genome Mamm Genome 11:120-30, 2000. Pubmed reference: 10656926. DOI: 10.1007/s003350010024.

1999

Vignaux, F., Priat, C., Jouquand, S., Hitte, C., Jiang, Z., Cheron, A., Renier, C., Andre, C., Galibert, F. :

Toward a dog radiation hybrid map Journal of Heredity 90:62-67, 1999. Pubmed reference: 9987906.

Langston, A.A., Mellersh, C.S., Wiegand, N.A., Acland, G.M., Ray, K., Aguirre, G.D., Ostrander, E.A. :

Toward a framework linkage map of the canine genome Journal of Heredity 90:7-14, 1999. Pubmed reference: 9987896.

Dolf, G., Batt, R., Baumle, E., Binns, M., Brenig, B., Bull, B., Dunner, S., Fredholm, M., Gaillard, C., Gerlach, J., Giger, U., Goldspink, G., Graphodatsky, A.S., Holmes, N., Judd, S., Juneja, K., Kelly, E.P., Kent, M.G., King, W.A., Lingaas, F., Long, S.E., Lubas, G., Mariat, D., Marki, U., Matthews, M., et al. :

DogMap: An international collaboration toward a low-resolution canine genetic marker map J Hered 90:3-6, 1999. Pubmed reference: 9987895. DOI: 10.1093/jhered/90.1.3.

Neff, M.W., Broman, K.W., Mellersh, C.S., Ray, K., Acland, G.M., Aguirre, G.D., Ziegle, J.S., Ostrander, E.A., Rine, J. :

A second-generation genetic linkage map of the domestic dog, Canis familiaris Genetics 151:803-820, 1999. Pubmed reference: 9927471.

Vignaux, F., Hitte, C., Priat, C., Chuat, J.C., Andre, C., Galibert, F. :

Construction and optimization of a dog whole-genome radiation hybrid panel Mammalian Genome 10:888-894, 1999. Pubmed reference: 10441740.

Werner, P., Mellersh, C.S., Raducha, M.G., DeRose, S., Acland, G.M., Prociuk, U., Wiegand, N., Aguirre, G.D., Henthorn, P.S., Patterson, D.F., Ostrander, E.A. :

Anchoring of canine linkage groups with chromosome-specific markers Mammalian Genome 10:814-823, 1999. Pubmed reference: 10430668.

Priat, C., Jiang, Z.H.H., Renier, C., Andre, C., Gailbert, F. :

Characterization of 463 Type I markers suitable for dog genome mapping Mammalian Genome 10:803-813, 1999. Pubmed reference: 10430667.

Yang, F., O'Brien, P.C.M., Milne, B.S., Graphodatsky, A.S., Solanky, N., Trifonov, V., Rens, W., Sargan, D., Ferguson-Smith, M.A. :

A complete comparative chromosome map for the dog, red fox, and human and its integration with canine genetic maps Genomics 62:189-202, 1999. Pubmed reference: 10610712. DOI: 10.1006/geno.1999.5989.

Lyons, L.A., Kehler, J.S., O'Brien, S.J. :

Development of comparative anchor tagged sequences (CATS) for canine genome mapping. J Hered 90:15-26, 1999. Pubmed reference: 9987897. DOI: 10.1093/jhered/90.1.15.

1998

Anon. :

Canine genetic linkage map just six months away Veterinary Record 142:383, 1998.

Anon. :

Cornell team helps put dog on the map Canine Practice 23:1 ff., 1998.

Priat, C., Hitte, C., Vignaux, F., Renier, C., Jiang, Z.H., Jouquand, S., Cheron, A., Andre, C., Galibert, F. :

A whole-genome radiation hybrid map of the dog genome Genomics 54:361-378, 1998. Pubmed reference: 9878239. DOI: 10.1006/geno.1998.5602.

1997

Lingaas, F., Sorensen, A., Juneja, R.K., Johansson, S., Fredholm, M., Wintero, A.K., Sampson, J., Mellersh, C., Curzon, A., Holmes, N.G., Binns, M.M., Dickens, H.F., Ryder, E.J., Gerlach, J., Baumle, E., Dolf, G. :

Towards construction of a canine linkage map - establishment of 16 linkage groups Mammalian Genome 8:218-221, 1997. Pubmed reference: 9069125.

Leveque, N.W. :

Canine genome mapping a dogged pursuit American Journal of Veterinary Research 58:936-937, 1997.

Mellersh, C.S., Langston, A.A., Acland, G.M., Fleming, M.A., Ray, K., Wiegand, N.A., Francisco, L.V., Gibbs, M., Aguirre, G.D., Ostrander, E.A. :

A linkage map of the canine genome Genomics 46:326-336, 1997. Pubmed reference: 9441735. DOI: 10.1006/geno.1997.5098.

1996

Anon. :

Canine genome project offers hope for the future Veterinary Record 138:406, 1996.

Reimann, N., Bartnitzke, S., Bullerdiek, J., Schmitz, U., Rogalla, P., Nolte, I., Rønne, M. :

An extended nomenclature of the canine karyotype. Cytogenet Cell Genet 73:140-4, 1996. Pubmed reference: 8646883. DOI: 10.1159/000134326.

Langford, C.F., Fischer, P.E., Binns, M.M., Holmes, N.G., Carter, N.P. :

Chromosome-specific paints from a high-resolution flow karyotype of the dog. Chromosome Res 4:115-23, 1996. Pubmed reference: 8785605. DOI: 10.1007/BF02259704.

Switoński, M., Reimann, N., Bosma, A.A., Long, S., Bartnitzke, S., Pieńkowska, A., Moreno-Milan, M.M., Fischer, P. :

Report on the progress of standardization of the G-banded canine (Canis familiaris) karyotype. Committee for the Standardized Karyotype of the Dog (Canis familiaris). Chromosome Res 4:306-9, 1996. Pubmed reference: 8817072. DOI: 10.1007/BF02263682.

1995

Graphodatsky, A.S., Beklemisheva, V.R., Dolf, G. :

High-resolution GTG-banding patterns of dog and silver fox chromosomes: description and comparative analysis. Cytogenet Cell Genet 69:226-31, 1995. Pubmed reference: 7698019. DOI: 10.1159/000133970.

1993

Miller, S.K. :

Search for Genes That Make Mans Best Friend New Scientist 138:5, 1993.

1991

Stone, D.M., Jacky, P.B., Prieur, D.J. :

The giemsa banding pattern of canine chromosomes, using a cell synchronization technique. Genome 34:407-12, 1991. Pubmed reference: 1889737. DOI: 10.1139/g91-062.

Morenomillan, M., Rodero, A., Alonso, F.J., Falcon, C. :

Contribution to the Establishment of the R-Banded Karyotype in Dogs. Genetics Selection Evolution 23:S179-S182, 1991.

1990

Poulsen, B.S., Shibasaki, Y., Ikeuchi, T., Rønne, M. :

Banding studies in Canis familiaris. I. Replication patterns in karyotypes from lymphocyte cultures. Cytobios 62:161-5, 1990. Pubmed reference: 1699707.

1989

Mellink, C.N.M., Bosma, A.A. :

The Karyotype of the Domestic Dog (Canis-Familiaris L). Cytogenetics of Animals, (ed. Halnan, C.R.E.) :151-157, 1989.

1975

Selden, J.R., Moorhead, P.S., Oehlert, M.L., Patterson, D.F. :

The Giemsa banding pattern of the canine karyotype. Cytogenet Cell Genet 15:380-7, 1975. Pubmed reference: 1225497. DOI: 10.1159/000130537.

1968

Borgaonkar, D.S., Elliot, O.S., Wong, M., Scott, J.P. :

Chromosome study of four breeds of dogs. J Hered 59:157-60, 1968. Pubmed reference: 5691532. DOI: 10.1093/oxfordjournals.jhered.a107670.

Caperea marginata (pygmy right whale) :

2023

Wolf, M., Zapf, K., Gupta, D.K., Hiller, M., Árnason, Ú., Janke, A. :

The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 21:79, 2023. Pubmed reference: 37041515. DOI: 10.1186/s12915-023-01579-1.

Capra aegagrus (wild goat) :

2015

Dong, Y., Zhang, X., Xie, M., Arefnezhad, B., Wang, Z., Wang, W., Feng, S., Huang, G., Guan, R., Shen, W., Bunch, R., McCulloch, R., Li, Q., Li, B., Zhang, G., Xu, X., Kijas, J.W., Salekdeh, G.H., Wang, W., Jiang, Y. :

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 16:431, 2015. Pubmed reference: 26044654. DOI: 10.1186/s12864-015-1606-1.

Capra hircus (goat) :

2025

Gou, Y., Jing, Y., Wang, Y., Li, X., Yang, J., Wang, K., He, H., Yang, Y., Tang, Y., Wang, C., Xu, J., Yang, F., Li, M., Tang, Q. :

Zhang, K., Zhao, J., Mi, S., Liu, J., Luo, J., Liu, J., Shi, H. :

Whole-genome variants resource of 298 Saanen dairy goats. Sci Data 12:528, 2025. Pubmed reference: 40157930. DOI: 10.1038/s41597-025-04880-6.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Sukhija, N., Kanaka, K.K., Ganguly, I., Dixit, S., Singh, S., Goli, R.C., Rathi, P., Nandini, P.B., Koloi, S. :

Cataloging copy number variation regions and allied diversity in goat breeds spanning pan India. Mamm Genome 36:523-540, 2025. Pubmed reference: 40175574. DOI: 10.1007/s00335-025-10122-2.

Zhao, J., Wang, Y., Kamalibieke, J., Gong, P., Zhang, F., Shi, H., Wang, W., Luo, J. :

Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat. BMC Genomics 26:377, 2025. Pubmed reference: 40234771. DOI: 10.1186/s12864-025-11576-z.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Zhang, J., Zhou, D., Yang, R., Guo, Z., Tian, X., Zhao, Y. :

Whole-genome sequencing and variants data of 304 indigenous goats from Southwest China. Sci Data 12:1595, 2025. Pubmed reference: 41027921. DOI: 10.1038/s41597-025-05893-x.

Tsoureki, A., Michailidou, S., Vouraki, S., Boukouvala, E., Arsenos, G., Sakaridis, I. :

Whole genome sequencing data of 14 indigenous Greek goats. Sci Data 12:1719, 2025. Pubmed reference: 41168259. DOI: 10.1038/s41597-025-05999-2.

2024

Belay, S., Belay, G., Nigussie, H., Jian-Lin, H., Tijjani, A., Ahbara, A.M., Tarekegn, G.M., Woldekiros, H.S., Mor, S., Dobney, K., Lebrasseur, O., Hanotte, O., Mwacharo, J.M. :

Whole-genome resource sequences of 57 indigenous Ethiopian goats. Sci Data 11:139, 2024. Pubmed reference: 38287052. DOI: 10.1038/s41597-024-02973-2.

Meng, Y., Zhang, W., Cheng, Y., Wu, Y., Wu, H., He, M., Chen, S., Man, C., Gao, H., Du, L., Chen, Q., Wang, F. :

Development and verification of a 10K liquid chip for Hainan black goat based on genotyping by pinpoint sequencing of liquid captured targets. BMC Genom Data 25:44, 2024. Pubmed reference: 38714950. DOI: 10.1186/s12863-024-01228-8.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

He, Q., Zhang, F., Zhang, X., Yao, W., Wu, J., Niu, H., Wang, Y., Luo, J. :

Chromosome-level dairy goat genome reveals the regulatory landscape of lactation. Int J Biol Macromol 280:135968, 2024. Pubmed reference: 39322167. DOI: 10.1016/j.ijbiomac.2024.135968.

Liu, J., Shi, Y., Mo, D., Luo, L., Xu, S., Lv, F. :

The goat pan-genome reveals patterns of gene loss during domestication. J Anim Sci Biotechnol 15:132, 2024. Pubmed reference: 39367490. DOI: 10.1186/s40104-024-01092-7.

Wang, Z., Lv, Q., Li, W., Huang, W., Gong, G., Yan, X., Liu, B., Chen, O., Wang, N., Zhang, Y., Wang, R., Li, J., Tian, S., Su, R. :

Chromosome-level genome assembly of the cashmere goat. Sci Data 11:1107, 2024. Pubmed reference: 39384835. DOI: 10.1038/s41597-024-03932-7.

Bian, P., Li, J., Zhou, S., Wang, X., Gong, M., Guo, X., Cai, Y., Yang, Q., Fu, J., Li, R., Huang, S., Luo, F., Shah, A.M., Lenstra, J.A., Mwacharo, J.M., Li, R., Ren, G., Wang, X., Li, C., Zheng, W., Jiang, Y., Wang, X. :

A graph-based goat pangenome reveals structural variations involved in domestication and adaptation. Mol Biol Evol 41:msae251, 2024. Pubmed reference: 39665690. DOI: 10.1093/molbev/msae251.

Wu, H., Luo, L.Y., Zhang, Y.H., Zhang, C.Y., Huang, J.H., Mo, D.X., Zhao, L.M., Wang, Z.X., Wang, Y.C., He-Hua, E., Bai, W.L., Han, D., Dou, X.T., Ren, Y.L., Dingkao, R., Chen, H.L., Ye, Y., Du, H.D., Zhao, Z.Q., Wang, X.J., Jia, S.G., Liu, Z.H., Li, M.H. :

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits. Nat Commun 15:10041, 2024. Pubmed reference: 39567477. DOI: 10.1038/s41467-024-54188-z.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Zhang, H., Liang, Y., Chen, S., Xuan, Z., Jiang, Y., Li, R., Cao, Y. :

Full-length transcriptome sequencing reveals extreme incomplete annotation of the goat genome. Anim Genet 54:421-424, 2023. Pubmed reference: 36849788. DOI: 10.1111/age.13311.

Arslan, M. :

Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). Mamm Genome 34:437-448, 2023. Pubmed reference: 37004528. DOI: 10.1007/s00335-023-09990-3.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

2021

Bhat, B., Ganai, N.A., Singh, A., Mir, R., Ahmad, S.M., Majeed Zargar, S., Malik, F. :

Changthangi Pashmina goat genome: Sequencing, assembly, and annotation. Front Genet 12:695178, 2021. Pubmed reference: 34354739. DOI: 10.3389/fgene.2021.695178.

2019

Wang, F.H., Zhang, L., Li, X.K., Fan, Y.X., Qiao, X., Gong, G., Yan, X.C., Zhang, L.T., Wang, Z.Y., Wang, R.J., Liu, Z.H., Wang, Z.X., He, L., Zhang, Y., Li, J.Q., Zhao, Y.H., Su, R. :

[Progress in goat genome studies]. Yi Chuan 41:928-938, 2019. Pubmed reference: 31624055. DOI: 10.16288/j.yczz.19-147.

Li, R., Fu, W., Su, R., Tian, X., Du, D., Zhao, Y., Zheng, Z., Chen, Q., Gao, S., Cai, Y., Wang, X., Li, J., Jiang, Y. :

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Front Genet 10:1169, 2019. Pubmed reference: 31803240. DOI: 10.3389/fgene.2019.01169.

2017

Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J.N., Huson, H.J., Nystrom, J.C., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisà, A., Ponce de León, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G.E., Dunham, M.J., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. :

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet 49:643-650, 2017. Pubmed reference: 28263316. DOI: 10.1038/ng.3802.

Worley, K.C. :

A golden goat genome. Nat Genet 49:485-486, 2017. Pubmed reference: 28358125. DOI: 10.1038/ng.3824.

2014

Du, X., Servin, B., Womack, J.E., Cao, J., Yu, M., Dong, Y., Wang, W., Zhao, S. :

An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae. BMC Genomics 15:625, 2014. Pubmed reference: 25052253. DOI: 10.1186/1471-2164-15-625.

2013

Dong, Y., Xie, M., Jiang, Y., Xiao, N., Du, X., Zhang, W., Tosser-Klopp, G., Wang, J., Yang, S., Liang, J., Chen, W., Chen, J., Zeng, P., Hou, Y., Bian, C., Pan, S., Li, Y., Liu, X., Wang, W., Servin, B., Sayre, B., Zhu, B., Sweeney, D., Moore, R., Nie, W., Shen, Y., Zhao, R., Zhang, G., Li, J., Faraut, T., Womack, J., Zhang, Y., Kijas, J., Cockett, N., Xu, X., Zhao, S., Wang, J., Wang, W. :

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol 31:135-41, 2013. Pubmed reference: 23263233. DOI: 10.1038/nbt.2478.

1998

Schibler, L., Vaiman, D., Oustry, A., Girauddelville, C., Cribiu, E.P. :

Comparative gene mapping - a fine-scale survey of chromosome rearrangements between ruminants and humans Genome Research 8:901-915, 1998. Pubmed reference: 9750190.

Umrikar, U.D., Natarajan, N., Thiagarajan, V., Narayankhedkar, S.G., Krishnan, A.R. :

Chromosome analysis of Indian domestic goat using high resolution GTG-banding technique. Indian Veterinary Journal 75:171-173, 1998.

1997

Yadav, B.R., Katiyar, P.K., Chauhan, M.S., Madan, M.L. :

Chromosome configuration during in vitro maturation of goat, sheep and buffalo oocytes. Theriogenology 47:943-51, 1997. Pubmed reference: 16728044. DOI: 10.1016/s0093-691x(97)00050-2.

1996

Vaiman, D., Schibler, L., Bourgeois, F., Oustry, A., Amigues, Y., Cribiu, E.P. :

A genetic linkage map of the male goat genome Genetics 144:279-305, 1996. Pubmed reference: 8878693.

Iannuzzi, L., Dimeo, G.P., Perucatti, A. :

G- and R-banded prometaphase karyotypes in goat (Capra hircus l). Caryologia 49:267-277, 1996.

1995

Bhatia, S., Shanker, V. :

Cytogenetic characteristics of Beetal goats. Indian Journal of Animal Sciences 65:592-595, 1995.

Deb, S.M., Biswas, J.C. :

Chromosome complements of Pashmina (Cashmere) goats. Indian Journal of Animal Sciences 65:472-473, 1995.

Umrikar, U.D., Natarajan, N., Thiagarajan, V., Narayanakhedkar, S.G., Krishnan, A.R. :

C and Q banding based karyotyping of Indian domestic goat. Indian Veterinary Journal 72:1162-1165, 1995.

1994

Kaftanovskaya, H.M., Serov, O.L. :

High-resolution GTG-banded chromosomes of cattle, sheep, and goat: a comparative study. J Hered 85:395-400, 1994. Pubmed reference: 7963454. DOI: 10.1093/oxfordjournals.jhered.a111485.

Iannuzzi, L., Di Meo, G.P., Perucatti, A. :

An improved characterization of goat chromosomes by means of G- and R-band comparison. Hereditas 120:245-51, 1994. Pubmed reference: 7928388. DOI: 10.1111/j.1601-5223.1994.00245.x.

Bhatia, S., Shanker, V. :

Y-Chromosome Polymorphism in Bengal Goats. Small Ruminant Research 13:55-61, 1994.

1993

Bhatia, S., Shanker, V. :

Somatic Chromosomes of Marwari Goats. Indian Journal of Animal Sciences 63:1302-1304, 1993.

Sharma, A., Balakrishnan, C.R. :

Meiotic Chromosomes of Jamunapari Bucks. Indian Journal of Animal Sciences 63:998-1000, 1993.

1992

Bhatia, S., Shanker, V. :

Alu 1 Restriction Enzyme Banding of Metaphase Chromosomes of Bengal Goats. Indian Journal of Animal Sciences 62:1057-1059, 1992.

Bhatia, S., Shanker, V. :

Chromosomal Profile of White Bengal Goats. Indian Journal of Animal Sciences 62:993-996, 1992.

1991

Burguete, I. :

Cytogenetic Study of the Spanish Goat Breed Murciana-Granadina Genetics Selection Evolution 23:S78-S80, 1991.

Hayes, H., Petit, E., Dutrillaux, B. :

Comparison of RBG-banded karyotypes of cattle, sheep, and goats. Cytogenet Cell Genet 57:51-5, 1991. Pubmed reference: 1855392. DOI: 10.1159/000133114.

Hayes, H., Petit, E. :

Comparison of RBG-Banded Karyotypes of Cattle, Sheep and Goat. Genetics Selection Evolution 23:S144-S147, 1991.

Bhatia, S., Shanker, V. :

Cytogenetic Analysis of Gaddi Goats. Indian Journal of Animal Sciences 61:646-648, 1991.

1990

DiBerardina, D., Hayes, H., Fries, R., Long, S. :

Bhat, P.P., Rawat, A.K. :

Banded Karyotypes of Indian Goat Breeds. Indian Journal of Animal Sciences 60:880-883, 1990.

1989

Bhatia, S., Shanker, V. :

Chromosome Analysis of Peripheral Leukocytes of Bengal Goat Indian Journal of Animal Sciences 59:1340-1342, 1989.

Mensher, S.H., Bunch, T.D., Maciulis, A. :

High-resolution G-banded karyotype and idiogram of the goat: a sheep-goat G-banded comparison. J Hered 80:150-5, 1989. Pubmed reference: 2926117. DOI: 10.1093/oxfordjournals.jhered.a110816.

1988

Cribiu, E.P., Matejka, M. :

Basis for a standardized karyotypic nomenclature and karyotypic variants in goats. Proceedings of the COGNOSAG Workshop 1986 :75-81, 1988.

Tsuda, S., Kotani, M., Shimaoka, T., Tanaka, K. :

[Chromosome analysis of the domestic goat using high-resolution G-banding techniques]. Japanese Journal of Zootechnical Science 59:1-11, 1988.

1987

Di Berardino, D., Ronne, M., Burguete, I., Lioi, M.B., Taibi, L., Matassino, D. :

R-banding pattern of the prometaphase chromosomes of the goat. J Hered 78:225-30, 1987. Pubmed reference: 3624843. DOI: 10.1093/oxfordjournals.jhered.a110371.

Cribiu, E.P., Matejka, M. :

Idiogram and standardized G-band karyotype of the goat (Capra hircus). Zuchthygiene 22:1-7, 1987.

Cribiu, E.P., Matejka, M. :

Standardized R-band karyotype of the goat (Capra hircus). Zuchthygiene 22:260-266, 1987.

1986

Pattnanayak, G.R., Patro, B.N. :

Chromosomes of Ganjam, Black Bengal and F1 (Ganjam X Black Bengal(goats Indian Journal of Heredity 18:37-46, 1986.

Cribiu, E.P., Lherm, C. :

[Normal karyotype and chromosomal anomalies in the domestic goat (Capra hircus)]. Receuil de Medecine Veterinaire 162:163-167, 1986.

Prakash, B. :

Chromosomal complements of Kamunapari and Barbari goats. Indian Journal of Animal Sciences 56:1073-1076, 1986.

1984

Hasanbasic, D., Kijajic, R., Milosevic, Z., Horsic, E. :

[The karyotype in goats]. Veterinaria, Yugoslavia 33:382-385, 1984.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1973

Hansen, K.M. :

Q-band karyotype of the goat (Capra hircus) and the relation between goat and bovine Q-bands. Hereditas 75:119-29, 1973. Pubmed reference: 4130421. DOI: 10.1111/j.1601-5223.1973.tb01148.x.

Capricornis milneedwardsii (Chinese serow) :

2024

Li, A., Yang, Q., Li, R., Cai, K., Zhu, L., Wang, X., Cheng, G., Wang, X., Lei, Y., Jiang, Y., Zan, L. :

Chromosome-level genome assembly for the Chinese serow (Capricornis milneedwardsii) provides insights into its taxonomic status and evolution. Ecol Evol 14:e70400, 2024. Pubmed reference: 39385836. DOI: 10.1002/ece3.70400.

Caranx ignobilis (giant trevally) :

2022

Pickett, B.D., Glass, J.R., Johnson, T.P., Ridge, P.G., Kauwe, J.S.K. :

The genome of a giant (trevally): Caranx ignobilis. GigaByte 2022:gigabyte67, 2022. Pubmed reference: 36824527. DOI: 10.46471/gigabyte.67.

Carassius auratus (goldfish) :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nat Genet 53:1493-1503, 2021. Pubmed reference: 34594040. DOI: 10.1038/s41588-021-00933-9.

2019

Omori, Y., Kon, T. :

Goldfish: an old and new model system to study vertebrate development, evolution and human disease. J Biochem 165:209-218, 2019. Pubmed reference: 30219851. DOI: 10.1093/jb/mvy076.

Carassius carassius (crucian carp) :

2025

Valencia-Pesqueira, L.M., Hoff, S.N.K., Tørresen, O.K., Jentoft, S., Lefevre, S. :

Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius. Sci Data 12:491, 2025. Pubmed reference: 40128231. DOI: 10.1038/s41597-025-04813-3.

Carassius gibelio (silver crucian carp) :

2025

Lian, K., Shan, J., Ma, J., Liu, Y., Li, X., Lu, M., Ding, M., Wei, J., Zhou, L., Kuang, Y., Gui, J., Peng, R. :

Chromosome-level genome assembly of Qihe gibel carp. Sci Data 12:1290, 2025. Pubmed reference: 40707488. DOI: 10.1038/s41597-025-05636-y.

Carcharhinus amblyrhynchos (grey reef shark) :

2025

Dahms, C., Vigliola, L., Cheung, L.H.T., Hui, J.H.L., Momigliano, P. :

Chromosome-level assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome. Genome Biol Evol 17:evaf176, 2025. Pubmed reference: 40971976. DOI: 10.1093/gbe/evaf176.

Carduelis pinus (pine siskin) :

2025

Cortez, J., Slade, J.W.G., Van Laar, T.A. :

Reference Genome of an Irruptive Migrant, the Pine Siskin (Spinus pinus). J Hered :esaf076, 2025. Pubmed reference: 41055600. DOI: 10.1093/jhered/esaf076.

Caretta caretta (Loggerhead turtle) :

2025

Yen, E.C., Gilbert, J.D., Balard, A., Taxonera, A., Fairweather, K., Ford, H.L., Thorburn, D.J., Rossiter, S.J., Martín-Durán, J.M., Eizaguirre, C. :

Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles. Gigascience 14:giaf054, 2025. Pubmed reference: 40478729. DOI: 10.1093/gigascience/giaf054.

Arantes, L.S., Brown, T., De Panis, D., Whiting, S.D., Young, E.J., LaCasella, E.L., Carvajal, G.A., Kennedy, A., Edmunds, D., Bentley, B.P., Balacco, J., Whelan, C., Jain, N., Tilley, T., O'Toole, B., Traore, P., Jarvis, E.D., Berry, O., Dutton, P.H., Komoroske, L.M., Mazzoni, C.J. :

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence. Gigascience 14:giaf105, 2025. Pubmed reference: 40971593. DOI: 10.1093/gigascience/giaf105.

2023

Chang, G., Jones, S., Leelakumari, S., Ashkani, J., Culibrk, L., O'Neill, K., Tse, K., Cheng, D., Chuah, E., McDonald, H., Kirk, H., Pandoh, P., Pari, S., Angelini, V., Kyle, C., Bertorelle, G., Zhao, Y., Mungall, A., Moore, R., Vilaça, S., Jones, S. :

The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. F1000Res 12:336, 2023. Pubmed reference: 37455852. DOI: 10.12688/f1000research.131283.2.

Carettochelys insculpta (pitted-shelled turtle) :

2024

Li, Y., Liu, Y., Zheng, J., Wu, B., Cui, X., Xu, W., Zhu, C., Qiu, Q., Wang, K. :

A chromosome-level genome assembly of the pig-nosed turtle (Carettochelys insculpta). Sci Data 11:311, 2024. Pubmed reference: 38521795. DOI: 10.1038/s41597-024-03157-8.

Carinascincus ocellatus (spotted skink) :

2025

Saunders, P.A., Sassi, F.M.C., Cioffi, M.B., Simakov, O., Burridge, C.P., Ezaz, T., Wapstra, E. :

Chromosome-level genome assembly and Oligo-FISH confirmation of chromosome models for the Tasmanian snow skink Carinascincus ocellatus (Scincidae, Eugongylinae). BMC Biol 23:300, 2025. Pubmed reference: 41063094. DOI: 10.1186/s12915-025-02402-9.

Carterodon sulcidens (Owl's spiny rat) :

2017

Di-Nizo, C.B., Banci, K.R.D.S., Sato-Kuwabara, Y., Silva, M.J.J. :

Advances in cytogenetics of Brazilian rodents: cytotaxonomy, chromosome evolution and new karyotypic data. Comp Cytogenet 11:833-892, 2017. Pubmed reference: 29362668. DOI: 10.3897/CompCytogen.v11i4.19925.

Castor canadensis (American beaver) :

1991

Ward, O.G., Graphodatsky, A.S., Wursterhill, D.H., Eremina, V.R., Park, J.P., Yu, Q. :

Cytogenetics of Beavers - A Case of Speciation by Monobrachial Centric Fusions. Genome 34:324-328, 1991.

Castor fiber (Eurasian beaver) :

1991

Ward, O.G., Graphodatsky, A.S., Wursterhill, D.H., Eremina, V.R., Park, J.P., Yu, Q. :

Cytogenetics of Beavers - A Case of Speciation by Monobrachial Centric Fusions. Genome 34:324-328, 1991.

Cavia porcellus (domestic guinea pig) :

2023

Borja Lozano, M.V., Vigil Santillán, B., More Montoya, M.J., Morón Barraza, J.A., García-Serquén, A.L., Gutiérrez Reynoso, G., Yalta-Macedo, C.E. :

Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes. Anim Genet 54:792-797, 2023. Pubmed reference: 37796666. DOI: 10.1111/age.13367.

Romanenko, S.A., Kliver, S.F., Serdyukova, N.A., Perelman, P.L., Trifonov, V.A., Seluanov, A., Gorbunova, V., Azpurua, J., Pereira, J.C., Ferguson-Smith, M.A., Graphodatsky, A.S. :

Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human. Sci Rep 13:21055, 2023. Pubmed reference: 38030702. DOI: 10.1038/s41598-023-46595-x.

1963

Sharma, G.P., Parshad, R., Ghuman, S.K. :

On the meiotic and somatic chromosomes of the guinea pig. Research Bulletin of the Panjab University of Science 14:167-169, 1963.

Centropyge bicolor (bicolor angelfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chromosome-level genome of butterflyfish unveils genomic features of unique color patterns and morphological traits. DNA Res 30:dsad018, 2023. Pubmed reference: 37590994. DOI: 10.1093/dnares/dsad018.

Centruroides vittatus :

2023

Yamashita, T., Rhoads, D.D., Pummill, J. :

A robust genome and assembly with transcriptomic data from the striped scorpion, Centruroides vittatus. bioRxiv , 2023. Pubmed reference: 37609349. DOI: 10.1101/2023.08.04.551372.

Cephalophus dorsalis (bay duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Chromosomal evolution in duiker antelope (Cephalophinae: Bovidae): karyotype comparisons, fluorescence in situ hybridization, and rampant X chromosome variation. Cytogenet Cell Genet 73:116-22, 1996. Pubmed reference: 8646878. DOI: 10.1159/000134321.

Cephalophus natalensis (Natal duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Cephalophus silvicultor (yellow-backed duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Cephalorhynchus hectori (Hector's dolphin) :

2025

Alvarez-Costes, S., Baker, C.S., Constantine, R., Carroll, E.L., Guhlin, J., Dutoit, L., Ferreira, S., Heimeier, D., Gemmell, N.J., Gillum, J., Hamner, R.M., Rayment, W., Roe, W., Te Aikā, B., Urban, L., Alexander, A. :

Leveraging synteny to generate reference genomes for conservation: Assembling the genomes of Hector's and Māui dolphins. Mol Ecol Resour 25:e14109, 2025. Pubmed reference: 40183628. DOI: 10.1111/1755-0998.14109.

Cerastes gasperettii :

2025

Mochales-Riaño, G., Hirst, S.R., Talavera, A., Burriel-Carranza, B., Pagone, V., Estarellas, M., Busschau, T., Boissinot, S., Hogan, M.P., Tena-Garcés, J., Pla, D., Calvete, J.J., Els, J., Margres, M.J., Carranza, S. :

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii). Gigascience 14:giaf030, 2025. Pubmed reference: 40478730. DOI: 10.1093/gigascience/giaf030.

Ceratotherium simum (white rhinoceros) :

2008

Trifonov, V.A., Stanyon, R., Nesterenko, A.I., Fu, B., Perelman, P.L., O'Brien, P.C., Stone, G., Rubtsova, N.V., Houck, M.L., Robinson, T.J., Ferguson-Smith, M.A., Dobigny, G., Graphodatsky, A.S., Yang, F. :

Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla. Chromosome Res 16:89-107, 2008. Pubmed reference: 18293107. DOI: 10.1007/s10577-007-1201-7.

1994

Houck, M.L., Ryder, O.A., Váhala, J., Kock, R.A., Oosterhuis, J.E. :

Diploid chromosome number and chromosomal variation in the white rhinoceros (Ceratotherium simum). J Hered 85:30-4, 1994. Pubmed reference: 8120356.

Ceratotherium simum cottoni (northern white rhinoceros) :

2025

Wang, G., Korody, M.L., Brändl, B., Hernandez-Toro, C.J., Rohrandt, C., Hong, K., Pang, A.W.C., Lee, J., Migliorelli, G., Stanke, M., Ford, S.M., Pollmann, I., Houck, M.L., Lewin, H.A., Lear, T.L., Ryder, O.A., Meissner, A., Loring, J.F., Müller, F.J. :

Genomic map of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni). Proc Natl Acad Sci U S A 122:e2401207122, 2025. Pubmed reference: 40359041. DOI: 10.1073/pnas.2401207122.

Cercopithecus lomamiensis (lesula) :

2025

Jensen, A., Horton, E.R., Koko, M.B., Detwiler, K.M., Guschanski, K. :

Holotype genome of the lesula provides insights into demography and evolution of a threatened primate lineage. Genome Biol 26:408, 2025. Pubmed reference: 41327385. DOI: 10.1186/s13059-025-03877-z.

Cervidae (deer) :

2023

Proskuryakova, A.A., Ivanova, E.S., Makunin, A.I., Larkin, D.M., Ferguson-Smith, M.A., Yang, F., Uphyrkina, O.V., Perelman, P.L., Graphodatsky, A.S. :

Comparative studies of X chromosomes in Cervidae family. Sci Rep 13:11992, 2023. Pubmed reference: 37491593. DOI: 10.1038/s41598-023-39088-4.

2002

Slate, J., Van Stijn, T.C., Anderson, R.M., McEwan, K.M., Maqbool, N.J., Mathias, H.C., Bixley, M.J., Stevens, D.R., Molenaar, A.J., Beever, J.E., Galloway, S.M., Tate, M.L. :

A deer (subfamily cervinae) genetic linkage map and the evolution of ruminant Genomes Genetics 160:1587-1597, 2002. Pubmed reference: 11973312.

1995

Tate, M.L., Mathias, H.C., Fennessy, P.F., Dodds, K.G., Penty, J.M., Hill, D.F. :

A new gene mapping resource: Interspecies hybrids between Pere David's deer (Elaphurus davidianus) and red deer (Cervus elaphus) Genetics 139:1383-1391, 1995. Pubmed reference: 7768446.

Cervus albirostris (white-lipped deer) :

2025

Yang, Y., Li, B., Luo, W., Xu, B., Luo, P., Zhang, T., You, Z. :

A high-quality Chromosome-level reference genome assembly of white-lipped deer (Przewalskium albirostris). Sci Data 12:727, 2025. Pubmed reference: 40312415. DOI: 10.1038/s41597-025-04796-1.

Cervus elaphus (red deer) :

2021

Vozdova, M., Kubickova, S., Cernohorska, H., Fröhlich, J., Rubes, J. :

Anchoring the CerEla1.0 genome assembly to red deer (Cervus elaphus) and cattle (Bos taurus) chromosomes and specification of evolutionary chromosome rearrangements in cervidae. Animals (Basel) 11:2614, 2021. Pubmed reference: 34573579. DOI: 10.3390/ani11092614.

2018

Bana, N.Á., Nyiri, A., Nagy, J., Frank, K., Nagy, T., Stéger, V., Schiller, M., Lakatos, P., Sugár, L., Horn, P., Barta, E., Orosz, L. :

The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes. Mol Genet Genomics 293:665-684, 2018. Pubmed reference: 29294181. DOI: 10.1007/s00438-017-1412-3.

2017

Johnston, S.E., Huisman, J., Ellis, P.A., Pemberton, J.M. :

A high-density linkage map reveals sexual dimorphism in recombination landscapes in red deer (Cervus elaphus). G3 (Bethesda) 7:2859-2870, 2017. Pubmed reference: 28667018. DOI: 10.1534/g3.117.044198.

1991

Herzog, S., Harrington, R. :

The role of hybridization in the karyotype evolution of deer (Cervidae; Artiodactyla; Mammalia). Theor Appl Genet 82:425-9, 1991. Pubmed reference: 24213258. DOI: 10.1007/BF00588595.

1986

Yu, X. :

[Comparative observations on the karyotype of northeastern red deer, northern silka deer and the offspring of five crossing combinations]. Acta Genetica Sinica 13:125-131, 1986.

Cervus nippon (sika deer) :

2025

Yang, Q., Xu, Y., Xiao, C., Dai, J., Zhan, J., Zhang, W. :

High-quality chromosome-scale genome assembly and annotation of Taohongling Sika deer (Cervus nippon kopschi). Sci Data 12:1839, 2025. Pubmed reference: 41261104. DOI: 10.1038/s41597-025-06122-1.

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Wang, Q., Han, R., Xing, H., Li, H. :

A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development. BMC Genomics 25:617, 2024. Pubmed reference: 38890595. DOI: 10.1186/s12864-024-10522-9.

Li, Z., Xu, Z., Zhu, L., Qin, T., Ma, J., Feng, Z., Yue, H., Guan, Q., Zhou, B., Han, G., Zhang, G., Li, C., Jia, S., Qiu, Q., Hao, D., Wang, Y., Wang, W. :

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration. Genome Res 35:188-201, 2024. Pubmed reference: 39542648. DOI: 10.1101/gr.279448.124.

1991

Herzog, S., Harrington, R. :

The role of hybridization in the karyotype evolution of deer (Cervidae; Artiodactyla; Mammalia). Theor Appl Genet 82:425-9, 1991. Pubmed reference: 24213258. DOI: 10.1007/BF00588595.

1986

Yu, X. :

[Comparative observations on the karyotype of northeastern red deer, northern silka deer and the offspring of five crossing combinations]. Acta Genetica Sinica 13:125-131, 1986.

Cetoscarus ocellatus (spotted parrotfish) :

2024

Tea, Y.K., Zhou, Y., Ewart, K.M., Cheng, G., Kawasaki, K., DiBattista, J.D., Ho, S.Y.W., Lo, N., Fan, S. :

The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus). Ecol Evol 14:e11148, 2024. Pubmed reference: 38476702. DOI: 10.1002/ece3.11148.

Chaenocephalus aceratus (blackfin icefish) :

2024

Lee, S.J., Kim, J., Choi, E.K., Jo, E., Cho, M., Kim, J.H., Park, H. :

Author Correction: A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data 11:47, 2024. Pubmed reference: 38191547. DOI: 10.1038/s41597-023-02861-1.

2023

Lee, S.J., Kim, J., Choi, E.K., Jo, E., Cho, M., Kim, J.H., Park, H. :

A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus. Sci Data 10:657, 2023. Pubmed reference: 37752129. DOI: 10.1038/s41597-023-02561-w.

Chaenodraco wilsoni (spiny icefish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Chaetodon auriga (threadfin butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chaetodon trifasciatus (melon butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chamaea fasciata :

2025

Benham, P.M., Cicero, C., Burns, K., Escalona, M., Beraut, E., Fairbairn, C.W., Seligmann, W.E., Marimuthu, M.P.A., Nguyen, O., Chumchim, N., Toffelmier, E., Nachman, M.W., Bowie, R.C.K. :

A highly contiguous genome assembly for the wrentit (Chamaea fasciata), the sole representative of the babbler radiation in the Americas. J Hered :esaf063, 2025. Pubmed reference: 40910567. DOI: 10.1093/jhered/esaf063.

Chamaeleo calyptratus (veiled chameleon) :

2024

Shylo, N., Price, A., Robb, S., Kupronis, R., Guzmán Méndez, I.A., DeGraffenreid, D., Gamble, T., Trainor, P. :

Chamaeleo calyptratus (veiled chameleon) chromosome-scale genome assembly and annotation provides insights into the evolution of reptiles and developmental mechanisms. bioRxiv , 2024. Pubmed reference: 39282430. DOI: 10.1101/2024.09.03.611012.

Champsocephalus esox (pike icefish) :

2023

Rivera-Colón, A.G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K.T., Yoon, V., Hüne, M., Gregory, S., Cheng, C.C., Catchen, J.M. :

Genomics of secondarily temperate adaptation in the only non-antarctic icefish. Mol Biol Evol 40:msad029, 2023. Pubmed reference: 36806940. DOI: 10.1093/molbev/msad029.

Champsocephalus gunnari (mackerel icefish) :

2023

Rivera-Colón, A.G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K.T., Yoon, V., Hüne, M., Gregory, S., Cheng, C.C., Catchen, J.M. :

Genomics of secondarily temperate adaptation in the only non-antarctic icefish. Mol Biol Evol 40:msad029, 2023. Pubmed reference: 36806940. DOI: 10.1093/molbev/msad029.

Channa argus (northern snakehead) :

2024

Sun, D., Wen, H., Qi, X., Li, C., Wang, L., Li, J., Zhu, M., Zhang, X., Li, Y. :

Chromosome-level genome assembly of the northern snakehead (Channa argus) using PacBio and Hi-C technologies. Sci Data 11:1437, 2024. Pubmed reference: 39730366. DOI: 10.1038/s41597-024-04314-9.

2017

Xu, J., Bian, C., Chen, K., Liu, G., Jiang, Y., Luo, Q., You, X., Peng, W., Li, J., Huang, Y., Yi, Y., Dong, C., Deng, H., Zhang, S., Zhang, H., Shi, Q., Xu, P. :

Draft genome of the Northern snakehead, Channa argus. Gigascience 6:1-5, 2017. Pubmed reference: 28327946. DOI: 10.1093/gigascience/gix011.

Channa asiatica (small snakehead) :

2025

Liu, H., Liu, J., Cui, T., Zhang, J., Luo, Q., Fei, S., Chen, K., Zhu, X., Ou, M., Zhao, J. :

A chromosome-level reference genome assembly of the Small snakehead (Channa asiatica). Sci Data 12:1159, 2025. Pubmed reference: 40628769. DOI: 10.1038/s41597-025-05479-7.

Chanodichthys mongolicus (Mongolian redfin) :

2025

Liu, Q., Wang, X., Yekefenhazi, D., Wang, J., Zhong, K., Zhang, Y., Fu, H., Zhou, Z., Huang, J., Li, W., Xu, X. :

Assembling chromosome-level genomes of male and female Chanodichthys mongolicus using PacBio HiFi reads and Hi-C technologies. Sci Data 12:949, 2025. Pubmed reference: 40481035. DOI: 10.1038/s41597-025-05120-7.

Charina bottae :

2022

Grismer, J.L., Escalona, M., Miller, C., Beraut, E., Fairbairn, C.W., Marimuthu, M.P.A., Nguyen, O., Toffelmier, E., Wang, I.J., Shaffer, H.B. :

Reference genome of the Rubber Boa, Charina bottae (Serpentes: Boidae). J Hered 113:641-648, 2022. Pubmed reference: 36056886. DOI: 10.1093/jhered/esac048.

Cheilinus chlorourus (floral wrasse) :

2025

Qu, J., Yang, X., Song, Z., Wang, S., Xing, Z., Wang, L., Wang, X. :

Chromosome-level genome assembly of Cheilinus chlorourus (Bloch, 1791) (Perciformes: Labridae). Sci Data 12:1133, 2025. Pubmed reference: 40603854. DOI: 10.1038/s41597-025-05288-y.

Cheilinus undulatus (humphead wrasse) :

2025

Zhang, K., Chen, J., Duan, B., You, C., Zhou, W., Zhao, Y., Yang, S., Wu, J., Shi, Q. :

A telomere-to-telomere gap-free genome assembly of the endangered humphead wrasse (Cheilinus undulatus). Sci Data 12:1194, 2025. Pubmed reference: 40646001. DOI: 10.1038/s41597-025-05475-x.

Cheilodactylus zonatus (blackbarred morwong) :

2025

Chang, M., Shi, K., Li, W., Ma, W., Chen, S., Sha, Z. :

Chromosome-level genome assembly and annotation of the spottedtail morwong (Cheilodactylus zonatus). Sci Data 12:1741, 2025. Pubmed reference: 41188244. DOI: 10.1038/s41597-025-06029-x.

Chelidonichthys spinosus (red gurnard) :

2023

Wang, Y., Zhang, H., Xian, W., Iwasaki, W. :

Chromosome genome assembly and annotation of the spiny red gurnard (Chelidonichthys spinosus). Sci Data 10:443, 2023. Pubmed reference: 37438353. DOI: 10.1038/s41597-023-02357-y.

Chelmon rostratus (copperband butterflyfish) :

2023

Zhang, S., Song, Y., Liu, M., Yuan, Z., Zhang, M., Zhang, H., Seim, I., Fan, G., Liu, S., Liu, X. :

Chelonia mydas (green sea turtle) :

2023

Dolfo, V., Boissin, E., Tatarata, M., Planes, S. :

Characterization of 25 new microsatellite markers for the green turtle (Chelonia mydas) and cross-species amplification in other marine turtle species. Mol Biol Rep 50:4145-4154, 2023. Pubmed reference: 36877349. DOI: 10.1007/s11033-023-08341-4.

Chelonoidis abingdonii (Abingdon island giant tortoise) :

2025

Jensen, E.L., Marchisio, C., Ochoa, A., Gray, R., Parra, V., Miller, J.M., Çilingir, F.G., Caccone, A. :

Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity. Ecol Evol 15:e71358, 2025. Pubmed reference: 40290375. DOI: 10.1002/ece3.71358.

Chiloscyllium griseum (grey bambooshark) :

2024

Harshan, P., Sukumaran, S., Gopalakrishnan, A. :

De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters. Sci Data 11:285, 2024. Pubmed reference: 38461175. DOI: 10.1038/s41597-024-03093-7.

Chionobathyscus dewitti :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Chiroptera (bats) :

2025

Wang, H., Zhou, H., Yao, X. :

Different species of bats: Genomics, transcriptome, and immune repertoire. Curr Issues Mol Biol 47:252, 2025. Pubmed reference: 40699651. DOI: 10.3390/cimb47040252.

Chlamydotis undulata (Houbara bustard) :

2024

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

2019

Mahiddine-Aoudjit, L., Boucekkine, O., Ladjali-Mohammedi, K. :

Banding cytogenetics of the vulnerable species Houbara bustard (Otidiformes) and comparative analysis with the Domestic fowl. Comp Cytogenet 13:1-17, 2019. Pubmed reference: 30701036. DOI: 10.3897/CompCytogen.v13i1.30660.

Chloebia gouldiae (Gouldian finch) :

2018

Toomey, M.B., Marques, C.I., Andrade, P., Araújo, P.M., Sabatino, S., Gazda, M.A., Afonso, S., Lopes, R.J., Corbo, J.C., Carneiro, M. :

A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch. Proc Biol Sci 285:20181788, 2018. Pubmed reference: 30282656. DOI: 10.1098/rspb.2018.1788.

Chlorocebus sabaeus (green monkey) :

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Choerodon schoenleinii (blackspot tuskfish) :

2025

Dong, Z., Gao, J., Zhao, Y., Gao, J., Guo, Y., Wang, Z., Zhang, N. :

Near telomere-to-telomere genome assembly of the blackspot tuskfish (Choerodon schoenleinii). Sci Data 12:537, 2025. Pubmed reference: 40164629. DOI: 10.1038/s41597-025-04893-1.

Chromidotilapia guntheri (Guenther's mouthbrooder) :

2024

Behrens, K.A., Koblmüller, S., Kocher, T.D. :

Genome assemblies for Chromidotilapia guntheri (Teleostei: Cichlidae) identify a novel candidate gene for vertebrate sex determination, RIN3. Front Genet 15:1447628, 2024. Pubmed reference: 39221227. DOI: 10.3389/fgene.2024.1447628.

Chrysolophus amherstiae (Lady Amherst's pheasant) :

2024

Garg, K.M., Dovih, P., Chattopadhyay, B. :

Hybrid de novo genome assembly of the sexually dimorphic Lady Amherst's pheasant. DNA Res 31:dsae001, 2024. Pubmed reference: 38168719. DOI: 10.1093/dnares/dsae001.

Ciconia boyciana (oriental stork) :

2024

Yang, S., Liu, Y., Zhao, X., Chen, J., Li, H., Liang, H., Fan, J., Zhou, M., Wang, S., Zhang, X., Shi, M., Han, L., Yu, M., Lu, Y., Liu, B., Xu, Y., Lan, T., Hou, Z. :

Genomic exploration of the endangered oriental stork, Ciconia boyciana, sheds light on migration adaptation and future conservation. Gigascience 13:giae081, 2024. Pubmed reference: 39435574. DOI: 10.1093/gigascience/giae081.

Cirrhinus molitorella (mud carp) :

2025

Tu, G., Yan, Z., Zhang, L., Liu, Z., Lv, Y., Li, Z., He, J., Weng, S., He, J., Wang, M. :

A chromosome-level genome assembly of the mud carp (Cirrhinus molitorella). Sci Data 12:285, 2025. Pubmed reference: 39962122. DOI: 10.1038/s41597-025-04615-7.

2024

Liu, H., Cui, T., Liu, H., Zhang, J., Luo, Q., Fei, S., Chen, K., Zhu, X., Zhu, C., Li, B., Fang, L., Zhao, J., Ou, M. :

Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing. Sci Data 11:1249, 2024. Pubmed reference: 39562583. DOI: 10.1038/s41597-024-04075-5.

Cirrhinus mrigala (mrigala) :

None

[No authors listed] :

Sci Data 11:898, None. Pubmed reference: 39154040. DOI: 10.1038/s41597-024-03747-6.

Clangula hyemalis (long-tailed duck) :

2024

Cádiz, M.I., Tengstedt, A.N.B., Sørensen, I.H., Pedersen, E.S., Fox, A.D., Hansen, M.M. :

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data. Evol Appl 17:e70008, 2024. Pubmed reference: 39257569. DOI: 10.1111/eva.70008.

Clarias batrachus (walking catfish) :

2023

Liu, K., Xie, N., Wang, Y., Liu, X. :

The utilization of reference-guided assembly and in silico libraries improves the draft genome of Clarias batrachus and Culter alburnus. Mar Biotechnol (NY) 25:907-917, 2023. Pubmed reference: 37661218. DOI: 10.1007/s10126-023-10248-x.

Clarias dussumieri :

2024

Mohindra, V., Chowdhury, L.M., Charan, R., Basheer, V.S., Jena, J. :

Genome sequencing and assembly of near threatened Clarias dussumieri (Valenciennes, 1840), an endemic catfish of peninsular India. Sci Data 11:1406, 2024. Pubmed reference: 39702573. DOI: 10.1038/s41597-024-04272-2.

Clarias fuscus (whitespotted clarias) :

2025

Chen, Y., Lin, X., Zhou, D., Zhang, Y., Wang, Q., Chen, H., Jiang, D., Deng, S., Li, G., Wang, P., Tian, C. :

An improved chromosome-level genome assembly and annotation of Hong Kong catfish (Clarias fuscus). Sci Data 12:193, 2025. Pubmed reference: 39893196. DOI: 10.1038/s41597-025-04523-w.

2023

Tian, C.X., Lin, X.H., Zhou, D.Y., Chen, Y., Shen, Y.J., Ye, M.H., Duan, C.Y., Zhang, Y.L., Yang, B.L., Deng, S.P., Zhu, C.H., Li, G.L. :

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region. BMC Genomics 24:291, 2023. Pubmed reference: 37254055. DOI: 10.1186/s12864-023-09394-2.

Clarias gariepinus (North African catfish) :

2024

Nguinkal, J.A., Zoclanclounon, Y.A.B., Brunner, R.M., Chen, Y., Goldammer, T. :

Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus). Sci Data 11:1095, 2024. Pubmed reference: 39375414. DOI: 10.1038/s41597-024-03906-9.

Clinocottus analis (woolly sculpin) :

2023

Wright, D.B., Escalona, M., Marimuthu, M.P.A., Sahasrabudhe, R., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Miller, C., Shaffer, H.B., Bernardi, G. :

Reference genome of the Woolly Sculpin, Clinocottus analis. J Hered 114:60-67, 2023. Pubmed reference: 36107748. DOI: 10.1093/jhered/esac055.

Clupea harengus (Atlantic herring) :

2019

Pettersson, M.E., Rochus, C.M., Han, F., Chen, J., Hill, J., Wallerman, O., Fan, G., Hong, X., Xu, Q., Zhang, H., Liu, S., Liu, X., Haggerty, L., Hunt, T., Martin, F.J., Flicek, P., Bunikis, I., Folkvord, A., Andersson, L. :

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Res 29:1919-1928, 2019. Pubmed reference: 31649060. DOI: 10.1101/gr.253435.119.

2016

Martinez Barrio, A., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., Dainat, J., Ekman, D., Höppner, M., Jern, P., Martin, M., Nystedt, B., Liu, X., Chen, W., Liang, X., Shi, C., Fu, Y., Ma, K., Zhan, X., Feng, C., Gustafson, U., Rubin, C.J., Sällman Almén, M., Blass, M., Casini, M., Folkvord, A., Laikre, L., Ryman, N., Ming-Yuen Lee, S., Xu, X., Andersson, L. :

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Elife 5, 2016. Pubmed reference: 27138043. DOI: 10.7554/eLife.12081.

Cnephaeus nilssonii (northern bat) :

2024

Laine, V.N., Pulliainen, A.T., Lilley, T.M. :

Reference genome for the Northern bat (Eptesicus nilssonii), a most northern bat species. J Hered 115:149-154, 2024. Pubmed reference: 37791665. DOI: 10.1093/jhered/esad056.

Cociella crocodila (crocodile flathead) :

2021

Zhao, R., Lu, Z., Cai, S., Gao, T., Xu, S. :

Whole genome survey and genetic markers development of crocodile flathead Cociella crocodilus. Anim Genet 52:891-895, 2021. Pubmed reference: 34486145. DOI: 10.1111/age.13136.

Coelodonta antiquitatis (woolly rhinoceros) :

2023

Seeber, P.A., Palmer, Z., Schmidt, A., Chagas, A., Kitagawa, K., Marinova-Wolff, E., Tafelmaier, Y., Epp, L.S. :

The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation. Biol Lett 19:20230343, 2023. Pubmed reference: 37909055. DOI: 10.1098/rsbl.2023.0343.

Coilia grayii (Gray's grenadier anchovy) :

2025

Fu, Z., Huang, J., Wang, L., Liang, X., Chen, Q., Hu, Y., Liu, J., Lu, J. :

A chromosome-level genome assembly of Gray's grenadier anchovy, Coilia grayii. Sci Data 12:656, 2025. Pubmed reference: 40251166. DOI: 10.1038/s41597-025-04834-y.

Coilia nasus (Japanese grenadier anchovy) :

2023

Ma, F., Wang, Y., Su, B., Zhao, C., Yin, D., Chen, C., Yang, Y., Wang, C., Luo, B., Wang, H., Deng, Y., Xu, P., Yin, G., Jian, J., Liu, K. :

Gap-free genome assembly of anadromous Coilia nasus. Sci Data 10:360, 2023. Pubmed reference: 37280262. DOI: 10.1038/s41597-023-02278-w.

Colinus virginianus (northern bobwhite) :

2024

Mussmann, S.M., Wilson, W.D. :

Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi. Mol Biol Rep 51:210, 2024. Pubmed reference: 38270754. DOI: 10.1007/s11033-023-09094-w.

Cololabis saira (Pacific saury) :

2024

Sato, M., Fukuda, K., Kadota, M., Makino-Itou, H., Tatsumi, K., Yamauchi, S., Kuraku, S. :

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology. DNA Res 31:dsae004, 2024. Pubmed reference: 38451834. DOI: 10.1093/dnares/dsae004.

Nakamura, Y., Yasuike, M., Fuji, T., Suyama, S., Mekuchi, M. :

Draft genome sequence and tissue expression panel of Pacific saury (Cololabis saira). DNA Res 31:dsae010, 2024. Pubmed reference: 38566577. DOI: 10.1093/dnares/dsae010.

Liu, Y., Luo, Y., Wang, P., Li, W., Tian, H., Cao, C., Ye, Z., Long, H., Lin, T., Wang, S., Yuan, X., Xiao, S., Watanabe, Y., Tian, Y. :

Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira. Commun Biol 7:1513, 2024. Pubmed reference: 39543266. DOI: 10.1038/s42003-024-07126-0.

Colossoma macropomum (tambaqui) :

2024

Agudelo, J.F.G., Mastrochirico-Filho, V.A., Garcia, B.F., Ariede, R.B., Yáñez, J.M., Valladão, G.M.R., Hashimoto, D.T. :

Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum. Genet Mol Biol 47:S1415-47572024000400203:e20230364, 2024. Pubmed reference: 39356131. DOI: 10.1590/1678-4685-GMB-2023-0364.

2021

Varela, E.S., Bekaert, M., Ganeco-Kirschnik, L.N., Torati, L.S., Shiotsuki, L., de Almeida, F.L., Villela, L.C.V., Rezende, F.P., da Silva Barroso, A., de Freitas, L.E.L., Taggart, J.B., Migaud, H. :

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum. BMC Genomics 22:709, 2021. Pubmed reference: 34598670. DOI: 10.1186/s12864-021-08037-8.

Columba guinea (speckled pigeon) :

2024

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid. G3 (Bethesda) 14:jkad280, 2024. Pubmed reference: 38066578. DOI: 10.1093/g3journal/jkad280.

2023

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid. bioRxiv , 2023. Pubmed reference: 37873124. DOI: 10.1101/2023.10.11.561892.

Columba livia (rock pigeon) :

2025

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

Yang, W., Zhou, H., Huang, J., Zhu, W., Hou, H., Li, H., Zhao, L., Zhang, J., Liu, J., Qin, C., Wang, L., Luo, H., Zhu, J., Xiao, F., Yao, J., Yang, C., Meng, H. :

Near telomere-to-telomere assembly of the Tarim pigeon (Columba livia) genome. Sci Data 11:1455, 2024. Pubmed reference: 39741153. DOI: 10.1038/s41597-024-04350-5.

2023

Wang, Y., Wang, X., Luo, Y., Zhang, J., Lin, Y., Wu, J., Zeng, B., Liu, L., Yan, P., Liang, J., Guo, H., Jin, L., Tang, Q., Long, K., Li, M. :

Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet 19:e1010746, 2023. Pubmed reference: 37289658. DOI: 10.1371/journal.pgen.1010746.

Maclary, E.T., Holt, C., Concepcion, G.T., Sović, I., Vickrey, A.I., Yandell, M., Kronenberg, Z., Shapiro, M.D. :

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

Conger myriaster (whitespotted conger) :

2025

Han, S., Li, C., Li, S., Chen, Y., Wang, C., Liu, K., Liu, Y., Wang, H.Y., Wang, Q., Cao, X., Shi, B., Shao, C. :

High-quality chromosome-level genome assembly of the whitespotted conger (Conger myriaster). Sci Data 12:626, 2025. Pubmed reference: 40234431. DOI: 10.1038/s41597-025-04947-4.

Conuropsis carolinensis (Carolina parakeet) :

2020

Evolutionary history, genomic adaptation to toxic diet, and extinction of the Carolina parakeet. Curr Biol 30:108-114.e5, 2020. Pubmed reference: 31839456. DOI: 10.1016/j.cub.2019.10.066.

Coregonus clupeaformis (lake whitefish) :

2024

Beemelmanns, A., Bouchard, R., Michaelides, S., Normandeau, E., Jeon, H.B., Chamlian, B., Babin, C., Hénault, P., Perrot, O., Harris, L.N., Zhu, X., Fraser, D., Bernatchez, L., Moore, J.S. :

Development of SNP panels from low-coverage whole genome sequencing (lcWGS) to support indigenous fisheries for three salmonid species in Northern Canada. Mol Ecol Resour 25:e14040, 2024. Pubmed reference: 39552382. DOI: 10.1111/1755-0998.14040.

Coregonus lavaretus (common whitefish) :

2025

Pokharel, K., Fischer, D., Iso-Touru, T., Tapio, I., Tapio, M., Leinonen, T., Kause, A. :

The genome assembly of the farmed European whitefish Coregonus lavaretus L. from the Finnish selective breeding programme. BMC Genom Data 26:22, 2025. Pubmed reference: 40128681. DOI: 10.1186/s12863-025-01313-6.

Coregonus ussuriensis (Amur whitefish) :

2024

Huang, T., Liu, E., Cao, B., Li, W., Wang, G., Gu, W., Ma, H., Dong, F., Wang, B., Xu, G. :

A chromosome-level genome assembly and evolutionary analysis of Coregonus ussuriensis Berg. Sci Data 11:792, 2024. Pubmed reference: 39025879. DOI: 10.1038/s41597-024-03642-0.

Coreius guichenoti :

2024

Zhou, C., Wang, Z., Wang, X., Qu, H., Song, Z. :

Chromosome-level genome assembly and genetic maker system of the endangered largemouth bronze gudgeon (Coreius guichenoti) with focus on conservation applications. Integr Zool 20:1061-1073, 2024. Pubmed reference: 39690135. DOI: 10.1111/1749-4877.12926.

Correlophus ciliatus (crested gecko) :

2024

Gumangan, M.A., Pan, Z., Lozito, T.P. :

Chromosome-level genome assembly and annotation of the crested gecko, Correlophus ciliatus, a lizard incapable of tail regeneration. GigaByte 2024:gigabyte140, 2024. Pubmed reference: 39539519. DOI: 10.46471/gigabyte.140.

Huang, R., Zhang, J., Lu, L., Huang, S., Li, C. :

High-quality genome assembly and annotation of the crested gecko (Correlophus ciliatus). G3 (Bethesda) 15:jkae265, 2024. Pubmed reference: 39545519. DOI: 10.1093/g3journal/jkae265.

Corynorhinus townsendii (Townsend's big-eared bat) :

2024

Capel, S.L.R., Hamilton, N.M., Fraser, D., Escalona, M., Nguyen, O., Sacco, S., Sahasrabudhe, R., Seligmann, W., Vazquez, J.M., Sudmant, P.H., Morrison, M.L., Wayne, R.K., Buchalski, M.R. :

Reference genome of Townsend's big-eared bat, Corynorhinus townsendii. J Hered 115:203-211, 2024. Pubmed reference: 38092381. DOI: 10.1093/jhered/esad078.

Coryphaena hippurus (common dolphinfish) :

2025

Hinojosa-Alvarez, S., Mendoza-Portillo, V., Chavez-Santoscoy, R.A., Hernández-Perez, J., Felix-Ceniceros, A., Magallón-Gayón, E., Mar-Silva, A.F., Ochoa-Zavala, M., Diaz-Jaimes, P. :

The draft genome assembly of the cosmopolitan pelagic fish dolphinfish (Coryphaena hippurus). G3 (Bethesda) 15:jkaf059, 2025. Pubmed reference: 40102961. DOI: 10.1093/g3journal/jkaf059.

Cottoperca gobio :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Cottoperca trigloides (channel bull blenny) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Coturnix coturnix (common quail) :

2025

Ravagni, S., Montero-Mendieta, S., Leonard, J.A., Webster, M.T., Christmas, M.J., Bunikis, I., Rodríguez-Teijeiro, J.D., Sanchez-Donoso, I., Vilà, C. :

Large inversions shape diversification and genome evolution in common quails. Mol Ecol 34:e17740, 2025. Pubmed reference: 40183764. DOI: 10.1111/mec.17740.

2024

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

Coturnix japonica (Japanese quail) :

2024

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

2020

Morris, K.M., Hindle, M.M., Boitard, S., Burt, D.W., Danner, A.F., Eory, L., Forrest, H.L., Gourichon, D., Gros, J., Hillier, L.W., Jaffredo, T., Khoury, H., Lansford, R., Leterrier, C., Loudon, A., Mason, A.S., Meddle, S.L., Minvielle, F., Minx, P., Pitel, F., Seiler, J.P., Shimmura, T., Tomlinson, C., Vignal, A., Webster, R.G., Yoshimura, T., Warren, W.C., Smith, J. :

The quail genome: insights into social behaviour, seasonal biology and infectious disease response. BMC Biol 18:14, 2020. Pubmed reference: 32050986. DOI: 10.1186/s12915-020-0743-4.

1991

de la Seña, C.A., Fechheimer, N.S., Nestor, K.E. :

Variability of C-banding patterns in Japanese quail chromosomes. Genome 34:993-7, 1991. Pubmed reference: 1778471. DOI: 10.1139/g91-153.

1989

Mayr, B., Lambrou, M., Schleger, W. :

Further resolution of the quail karyotype and characterization of microchromosomes by counterstain-enhanced fluorescence. J Hered 80:147-50, 1989. Pubmed reference: 2494254. DOI: 10.1093/oxfordjournals.jhered.a110815.

Schmid, M., Enderle, E., Schindler, D., Schempp, W. :

Chromosome banding and DNA replication patterns in bird karyotypes. Cytogenet Cell Genet 52:139-46, 1989. Pubmed reference: 2630186. DOI: 10.1159/000132864.

1985

Baumgartner, J., Koncekova, Z. :

[A karyological study of the Japanese quail]. Vedecke Prace - Hydinarstvo :37-45, 1985.

Yoshizawa, M., Noguchi, I., Muramatsu, T., Okamoto, A. :

Karyological sexing and sex ratio of Japanese quail embryos. Japanese Journal of Animal Reproduction 31:236-243, 1985.

Cranoglanis bouderius :

2022

Xu, Y., Shao, F., Chen, W., Ni, L., Peng, Z. :

A chromosome-level genome of the helmet catfish (Cranoglanis bouderius). Front Genet 13:962406, 2022. Pubmed reference: 36035162. DOI: 10.3389/fgene.2022.962406.

Cricetulus griseus (Chinese hamster) :

2025

Sun, M., Guo, Y., Ren, Z., Song, A., Lu, J., Li, C., Lv, J., Guo, M., Liu, X., Du, X., Chen, Z., Song, G., He, Y., Chen, Z., Huo, X. :

Development of a single-nucleotide polymorphism panel genotyping system for genetic analysis of Chinese hamsters. Animal Model Exp Med 8:916-921, 2025. Pubmed reference: 40016881. DOI: 10.1002/ame2.70006.

Cricetus cricetus (black-bellied hamster) :

2025

Reiners, T.E., Prochotta, D., Schell, T., Greve, C., Hamadou, A.B., Gerheim, C., Ortega, J.M., Nowak, C., Nebenführ, M., Janke, A. :

Chromosome-level genome of the European hamster (Cricetus cricetus) and its genome-wide population structure across Western Europe. BMC Biol 23:276, 2025. Pubmed reference: 40954469. DOI: 10.1186/s12915-025-02384-8.

Crocodylus cf. rhombifer :

2024

Meredith, R.W., Milián-García, Y., Gatesy, J., Russello, M.A., Amato, G. :

Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome. BMC Genom Data 25:53, 2024. Pubmed reference: 38844844. DOI: 10.1186/s12863-024-01240-y.

Crocodylus porosus (Australian saltwater crocodile) :

2020

Ghosh, A., Johnson, M.G., Osmanski, A.B., Louha, S., Bayona-Vásquez, N.J., Glenn, T.C., Gongora, J., Green, R.E., Isberg, S., Stevens, R.D., Ray, D.A. :

A high-quality reference genome assembly of the saltwater crocodile, Crocodylus porosus, reveals patterns of selection in crocodylidae. Genome Biol Evol 12:3635-3646, 2020. Pubmed reference: 31821505. DOI: 10.1093/gbe/evz269.

2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Crocuta crocuta (spotted hyena) :

2023

Seeber, P.A., Palmer, Z., Schmidt, A., Chagas, A., Kitagawa, K., Marinova-Wolff, E., Tafelmaier, Y., Epp, L.S. :

Cromileptes altivelis (humpback grouper) :

2024

Liu, J., Sun, H., Tang, L., Wang, Y., Wang, Z., Mao, Y., Huang, H., Zhang, Q. :

Chromosome-level genome assembly of humpback grouper using PacBio HiFi reads and Hi-C technologies. Sci Data 11:51, 2024. Pubmed reference: 38195804. DOI: 10.1038/s41597-023-02907-4.

Crossoptilon crossoptilon (white-eared pheasant) :

2024

Wu, S., Wang, K., Dou, T., Yuan, S., Wu, D.D., Ge, C., Jia, J., Su, Z. :

High-quality genome assembly of a C. crossoptilon and related functional and genetics data resources. Sci Data 11:247, 2024. Pubmed reference: 38413610. DOI: 10.1038/s41597-024-03087-5.

Crotalus adamanteus (eastern diamondback rattlesnake) :

2025

Nachtigall, P.G., Nystrom, G.S., Broussard, E.M., Wray, K.P., Junqueira-de-Azevedo, I.L.M., Parkinson, C.L., Margres, M.J., Rokyta, D.R. :

A segregating structural variant defines novel venom phenotypes in the eastern diamondback rattlesnake. Mol Biol Evol 42:msaf058, 2025. Pubmed reference: 40101100. DOI: 10.1093/molbev/msaf058.

Crotalus horridus (timber rattlesnake) :

2024

Roseman, M.A., Mason, A.J., Bode, E.R., Bolton, P.E., Nachtigall, P.G., Peterman, W.E., Gibbs, H.L. :

Insights from the timber rattlesnake (Crotalus horridus) genome for MHC gene architecture and evolution in threatened rattlesnakes. J Hered 116:591-602, 2024. Pubmed reference: 39704347. DOI: 10.1093/jhered/esae075.

Crotalus oreganus :

2023

Westeen, E.P., Escalona, M., Holding, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Perri, R., Fisher, R.N., Toffelmier, E., Shaffer, H.B., Wang, I.J. :

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex. J Hered 114:681-689, 2023. Pubmed reference: 37493092. DOI: 10.1093/jhered/esad045.

Crotalus ruber (red diamond rattlesnake) :

2024

Hirst, S.R., Rautsaw, R.M., VanHorn, C.M., Beer, M.A., McDonald, P.J., Rosales-García, R.A., Lopez, B.R., Rubio Rincón, A., Franz-Chávez, H., Vásquez-Cruz, V., Kelly-Hernández, A., Storfer, A., Borja, M., Castañeda-Gaytán, G., Frandsen, P.B., Parkinson, C.L., Strickland, J.L., Margres, M.J. :

Where the 'ruber' meets the road: Using the genome of the Red Diamond Rattlesnake to unravel the evolutionary processes driving venom evolution. Genome Biol Evol 16:evae198, 2024. Pubmed reference: 39255072. DOI: 10.1093/gbe/evae198.

Ctenopharyngodon idella (grass carp) :

2025

Liu, F., Li, Y., Wang, G., Zhang, D., Yang, X., Zhou, C., Zhou, R., Liu, H. :

The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement. Gigascience 14:giaf059, 2025. Pubmed reference: 40531666. DOI: 10.1093/gigascience/giaf059.

[No authors listed] :

Correction to: The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement. Gigascience 14:giaf088, 2025. Pubmed reference: 40665468. DOI: 10.1093/gigascience/giaf088.

Culter alburnus (topmouth culter) :

2024

Zhao, H., Fang, D.A., Wang, Y., Zhang, M., Wang, A., Xu, Y., Xu, D. :

A high-quality chromosome-level genome assembly of the topmouth culter (Culter alburnus Basilewsky, 1855). Sci Data 11:910, 2024. Pubmed reference: 39174585. DOI: 10.1038/s41597-024-03657-7.

2023

Liu, K., Xie, N., Wang, Y., Liu, X. :

Cyanistes caeruleus (Blue tit) :

2010

Hansson, B., Ljungqvist, M., Dawson, DA., Mueller, JC., Olano-Marin, J., Ellegren, H., Nilsson, JA. :

Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus). Heredity 104:67-78, 2010. Pubmed reference: 19707235. DOI: 10.1038/hdy.2009.107.

Cyanocitta stelleri (Steller's jay) :

2023

Benham, P.M., Cicero, C., DeRaad, D.A., McCormack, J.E., Wayne, R.K., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., Bowie, R.C.K. :

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri). J Hered 114:549-560, 2023. Pubmed reference: 37395718. DOI: 10.1093/jhered/esad042.

Cygnus atratus (black swan) :

2023

Chong, Y., Tu, X., Lu, Y., Gao, Z., He, X., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Two high-quality Cygnus genome assemblies reveal genomic variations associated with plumage color. Int J Mol Sci 24:16953, 2023. Pubmed reference: 38069278. DOI: 10.3390/ijms242316953.

Cygnus olor (mute swan) :

2023

Chong, Y., Tu, X., Lu, Y., Gao, Z., He, X., Hong, J., Wu, J., Wu, D., Xi, D., Deng, W. :

Two high-quality Cygnus genome assemblies reveal genomic variations associated with plumage color. Int J Mol Sci 24:16953, 2023. Pubmed reference: 38069278. DOI: 10.3390/ijms242316953.

Cylindrophis ruffus (red cylinder snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Cynomys gunnisoni (Gunnison's prairie dog) :

2020

Tsuchiya, M.T.N., Dikow, R.B., Cassin-Sackett, L. :

First genome sequence of the Gunnison's prairie dog (Cynomys gunnisoni), a keystone species and player in the transmission of sylvatic plague. Genome Biol Evol 12:618-625, 2020. Pubmed reference: 32277812. DOI: 10.1093/gbe/evaa069.

Cyprinus carpio (common carp) :

2025

Yuan, J., Li, J., Yong, J., Liao, X., Guo, H., Niu, Y. :

A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology. Gigascience 14:giaf087, 2025. Pubmed reference: 40880134. DOI: 10.1093/gigascience/giaf087.

Li, Z., Wang, Z., Peng, Y., Hu, Y., Zhou, X. :

A high-quality chromosome-level genome assembly of the common carp (Cyprinus carpio var. Xiangxi). Sci Data 12:1639, 2025. Pubmed reference: 41083452. DOI: 10.1038/s41597-025-05927-4.

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

2014

Xu, P., Zhang, X., Wang, X., Li, J., Liu, G., Kuang, Y., Xu, J., Zheng, X., Ren, L., Wang, G., Zhang, Y., Huo, L., Zhao, Z., Cao, D., Lu, C., Li, C., Zhou, Y., Liu, Z., Fan, Z., Shan, G., Li, X., Wu, S., Song, L., Hou, G., Jiang, Y., Jeney, Z., Yu, D., Wang, L., Shao, C., Song, L., Sun, J., Ji, P., Wang, J., Li, Q., Xu, L., Sun, F., Feng, J., Wang, C., Wang, S., Wang, B., Li, Y., Zhu, Y., Xue, W., Zhao, L., Wang, J., Gu, Y., Lv, W., Wu, K., Xiao, J., Wu, J., Zhang, Z., Yu, J., Sun, X. :

Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 46:1212-9, 2014. Pubmed reference: 25240282. DOI: 10.1038/ng.3098.

2013

Zhao, L., Zhang, Y., Ji, P., Zhang, X., Zhao, Z., Hou, G., Huo, L., Liu, G., Li, C., Xu, P., Sun, X. :

A dense genetic linkage map for common carp and its integration with a BAC-based physical map. PLoS One 8:e63928, 2013. Pubmed reference: 23704958. DOI: 10.1371/journal.pone.0063928.

Cyprinus rubrofuscus :

2025

Bian, C., Huan, R., Shi, Q. :

Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes. Gigascience 14:giaf073, 2025. Pubmed reference: 40720841. DOI: 10.1093/gigascience/giaf073.

Dama dama (fallow deer) :

1994

Lioi, M.B., Scarfi, M.R., Di Berardino, D. :

The RBA-banded karyotype of the fallow deer (Dama dama L.). Cytogenet Cell Genet 67:75-80, 1994. Pubmed reference: 8039426. DOI: 10.1159/000133803.

1993

Gripenberg, U., Wessman, M. :

Restriction Endonuclease Staining Profiles in the C- Heterochromatin of Cervidae. Hereditas 118:251-257, 1993.

1990

Rubini, M., Negri, E., Fontana, F. :

Standard karyotype and chromosomal evolution of the fallow deer (Dama dama L.). Cytobios 64:155-61, 1990. Pubmed reference: 2090390.

Herzog, S. :

Constitutive Heterochromatin in the Fallow Deer (Cervus-Dama). Zeitschrift Fur Saugetierkunde-International Journal of Mammalian Biology 55:63-65, 1990.

Damaliscus lunatus (topi) :

1996

Kumamoto, A.T., Charter, S.J., Houck, M.L., Frahm, M. :

Chromosomes of Damaliscus (Artiodactyla, Bovidae): simple and complex centric fusion rearrangements. Chromosome Res 4:614-21, 1996. Pubmed reference: 9024978. DOI: 10.1007/BF02261724.

Damaliscus pygargus :

1996

Kumamoto, A.T., Charter, S.J., Houck, M.L., Frahm, M. :

Chromosomes of Damaliscus (Artiodactyla, Bovidae): simple and complex centric fusion rearrangements. Chromosome Res 4:614-21, 1996. Pubmed reference: 9024978. DOI: 10.1007/BF02261724.

Danio rerio (zebrafish) :

1999

Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., Talbot, W.S. :

A genetic linkage map for zebrafish: Comparative analysis and localization of genes and expressed sequences Genome Research 9:334-347, 1999. Pubmed reference: 10207156.

1998

Knapik, E.W., Goodman, A., Ekker, M., Chevrette, M., Delgado, J., Neuhauss, S., Shimoda, N., Driever, W., Fishman, M.C., Jacob, H.J. :

A microsatellite genetic linkage map for zebrafish (danio rerio) Nature Genetics 18:338-343, 1998. Pubmed reference: 9537415. DOI: 10.1038/ng0498-338.

Postlethwait, J.H., Yan, Y.L., Gates, M.A., Horne, S., Amores, A., Brownlie, A., Donovan, A., Egan, E.S., Force, A., Gong, Z.Y., Goutel, C., Fritz, A., Kelsh, R., Knapik, E., Liao, E., Paw, B., Ransom, D., Singer, A., Thomson, M., Abduljabbar, T.S., Yelick, P., Beier, D., Joly, J.S., Larhammar, D., Rosa, F., et al. :

Vertebrate genome evolution and the zebrafish gene map Nature Genetics 18:345-349, 1998. Pubmed reference: 9537416. DOI: 10.1038/ng0498-345.

1996

Johnson, S.L., Gates, M.A., Johnson, M., Talbot, W.S., Horne, S., Baik, K., Rude, S., Wong, J.R., Postlethwait, J.H. :

Centromere-linkage analysis and consolidation of the zebrafish genetic map Genetics 142:1277-1288, 1996. Pubmed reference: 8846904.

Dascyllus trimaculatus (three spot damselfish) :

2023

Roberts, M.B., Schultz, D.T., Gatins, R., Escalona, M., Bernardi, G. :

Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus. G3 (Bethesda) 13:jkac339, 2023. Pubmed reference: 36905099. DOI: 10.1093/g3journal/jkac339.

Dasyurus viverrinus (southeastern quoll) :

2024

Hartley, G.A., Frankenberg, S.R., Robinson, N.M., MacDonald, A.J., Hamede, R.K., Burridge, C.P., Jones, M.E., Faulkner, T., Shute, H., Rose, K., Brewster, R., O'Neill, R.J., Renfree, M.B., Pask, A.J., Feigin, C.Y. :

Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Commun Biol 7:636, 2024. Pubmed reference: 38796620. DOI: 10.1038/s42003-024-06251-0.

Daubentonia madagascariensis (aye-aye) :

2024

Versoza, C.J., Pfeifer, S.P. :

A hybrid genome assembly of the endangered aye-aye (Daubentonia madagascariensis). G3 (Bethesda) 14:jkae185, 2024. Pubmed reference: 39109845. DOI: 10.1093/g3journal/jkae185.

Versoza, C.J., Jensen, J.D., Pfeifer, S.P. :

The landscape of structural variation in aye-ayes (Daubentonia madagascariensis). bioRxiv , 2024. Pubmed reference: 39605644. DOI: 10.1101/2024.11.08.622672.

Decapterus maruadsi (Japanese scad) :

2024

Chen, L., Zhou, Z., Zhou, Z., Yang, J., Deng, Y., Bai, Y., Pu, F., Zhou, T., Xu, P. :

Chromosome-level assembly and gene annotation of Decapterus maruadsi genome using Nanopore and Hi-C technologies. Sci Data 11:69, 2024. Pubmed reference: 38218740. DOI: 10.1038/s41597-024-02912-1.

Deinagkistrodon acutus (Chinese moccasin) :

2023

Wang, X., Liu, L., Zhu, W., Wang, S., Shi, M., Yang, S., Lu, H., Cao, J. :

Genome assembly and annotation of the sharp-nosed pit viper Deinagkistrodon acutus based on next-generation sequencing data. GigaByte 2023:gigabyte88, 2023. Pubmed reference: 37711277. DOI: 10.46471/gigabyte.88.

Delichon dasypus (Asian house martin) :

2024

Chan, Y.F., Lu, C.W., Kuo, H.C., Hung, C.M. :

A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3 (Bethesda) 14:jkae077, 2024. Pubmed reference: 38607414. DOI: 10.1093/g3journal/jkae077.

Delphinus delphis (saddleback dolphin) :

2024

Ding, K., Xu, Q., Zhao, L., Li, Y., Li, Z., Shi, W., Zeng, Q., Wang, X., Zhang, X. :

Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis). BMC Genomics 25:373, 2024. Pubmed reference: 38627659. DOI: 10.1186/s12864-024-10268-4.

Desmognathus fuscus (dusky salamander) :

2025

Myers, E.A., Stewart, A.A., O'Brien, A.E., Smith, J.J., Pyron, R.A. :

The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus). G3 (Bethesda) 15:jkaf157, 2025. Pubmed reference: 40619733. DOI: 10.1093/g3journal/jkaf157.

Diadophis punctatus (Ringneck snake) :

2023

Westeen, E.P., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Fisher, R.N., Toffelmier, E., Shaffer, H.B., Wang, I.J. :

A reference genome assembly for the continentally-distributed ring-necked snake, Diadophis punctatus. J Hered 114:690-697, 2023. Pubmed reference: 37688363. DOI: 10.1093/jhered/esad051.

Diceros bicornis (black rhinoceros) :

2024

Kraaijeveld, K., Bossers, K., Petrusevski, N., Pieterman, S., Bruins-van Sonsbeek, L.G.R., Wittink, F. :

ONT read assembly of the black rhino genome. BMC Genom Data 25:27, 2024. Pubmed reference: 38443836. DOI: 10.1186/s12863-024-01214-0.

Diomedea antipodensis :

2025

Foote, I., Oosting, T., Walker, K., Elliott, G., Rexer-Huber, K., Parker, G.C., Chambers, G.K., Ritchie, P.A. :

Genome assembly of the Antipodean and Gibson's albatrosses (Diomedea antipodensis antipodensis and D. a. gibsoni). J Hered :esaf054, 2025. Pubmed reference: 40795279. DOI: 10.1093/jhered/esaf054.

Diplodus puntazzo (sharpsnout seabream) :

2025

Pegueroles, C., Galià-Camps, C., Pascual, M., Bassitta, M., González, D., Greve, C., Macpherson, E., Raventós, N., Schell, T., Torrado, H., Carreras, C. :

Chromosome-level genome assembly and annotation of the sharpsnout seabream (Diplodus puntazzo). Sci Data 12:576, 2025. Pubmed reference: 40185799. DOI: 10.1038/s41597-025-04902-3.

Dipodomys merriami (Merriam's kangaroo rat) :

2025

Voss, E.R., Escalona, M., Nguyen, O., Marimuthu, M.P.A., Chumchim, N., Fairbairn, C.W., Seligmann, W., Beraut, E., Conroy, C.J., Patton, J.L., Bowie, R.C.K., Nachman, M.W. :

A high-quality genome assembly for a desert-adapted rodent, Merriam's kangaroo rat (Dipodomys merriami). J Hered 116:524-531, 2025. Pubmed reference: 40243028. DOI: 10.1093/jhered/esaf023.

Discogobio brachyphysallidos :

2024

Zheng, L.P., Wu, L.L., Sun, H.Y. :

Chromosome-level genome assembly of Discogobio brachyphysallidos (Teleostei, Cyprinidae) and population genomics of the D. brachyphysallidos complex: Impacts of geological and climate changes on species evolution in Southwest China. Int J Mol Sci 25:13462, 2024. Pubmed reference: 39769226. DOI: 10.3390/ijms252413462.

Dissostichus eleginoides (Patagonian toothfish) :

2024

Ryder, D., Stone, D., Minardi, D., Riley, A., Avant, J., Cross, L., Soeffker, M., Davidson, D., Newman, A., Thomson, P., Darby, C., van Aerle, R. :

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 25:233, 2024. Pubmed reference: 38438840. DOI: 10.1186/s12864-024-10141-4.

Lee, S.J., Cho, M., Kim, J., Choi, E., Choi, S., Chung, S., Lee, J., Kim, J.H., Park, H. :

Chromosome-level genome assembly and annotation of the Patagonian toothfish Dissostichus eleginoides. Sci Data 11:1240, 2024. Pubmed reference: 39550355. DOI: 10.1038/s41597-024-04119-w.

Distichodus sexfasciatus (sixbar distichodus) :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Dolloidraco longedorsalis :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Dugong dugon (dugong) :

2024

Baker, D.N., Abueg, L., Escalona, M., Farquharson, K.A., Lanyon, J.M., Le Duc, D., Schöneberg, T., Absolon, D., Sims, Y., Fedrigo, O., Jarvis, E.D., Belov, K., Hogg, C.J., Shapiro, B. :

A chromosome-level genome assembly for the dugong (Dugong dugon). J Hered 115:212-220, 2024. Pubmed reference: 38245832. DOI: 10.1093/jhered/esae003.

Tian, R., Zhang, Y., Kang, H., Zhang, F., Jin, Z., Wang, J., Zhang, P., Zhou, X., Lanyon, J.M., Sneath, H.L., Woolford, L., Fan, G., Li, S., Seim, I. :

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 15:5568, 2024. Pubmed reference: 38956050. DOI: 10.1038/s41467-024-49769-x.

Dysomma anguillare (shortbelly eel) :

2024

Yang, T.Y., Zhu, Z.Y., Liu, Y.P., Wang, S.G. :

The first genome-wide survey of shortbelly eel (Dysomma anguillare Barnard, 1923) to provide genomic characteristics, microsatellite markers and complete mitogenome information. Biochem Genet 62:2296-2313, 2024. Pubmed reference: 37906301. DOI: 10.1007/s10528-023-10543-1.

Echeneis naucrates (live sharksucker) :

2024

Gao, T., Liu, K., Liu, Q., Wang, D. :

An improved chromosome-level genome assembly and annotation of Echeneis naucrates. Sci Data 11:452, 2024. Pubmed reference: 38704456. DOI: 10.1038/s41597-024-03309-w.

Elaphe carinata :

2023

Fan, J., Huang, R., Yang, D., Gong, Y., Cui, Z., Wang, X., Su, Z., Yu, J., Zhang, Y., Zhang, T., Jiang, Z., Lan, T., Wang, H., Huang, S. :

Genome assembly and annotation of the king ratsnake, Elaphe carinata. GigaByte 2023:gigabyte101, 2023. Pubmed reference: 38098688. DOI: 10.46471/gigabyte.101.

Elaphe schrenckii :

2025

Zhu, Z., Yang, X., Kang, W., Cai, C., Zhou, Q. :

Chromosome-level genome assembly and annotation of the Amur rat snake Elaphe schrenckii. Genome Biol Evol 17:evaf086, 2025. Pubmed reference: 40333365. DOI: 10.1093/gbe/evaf086.

Elaphe taeniura (beauty snake) :

2025

Chen, J., Liu, Q., Tan, S., Guo, P., Du, L. :

A chromosome-level genome assembly and annotation for the beauty snake Elaphe taeniura. J Hered :esaf055, 2025. Pubmed reference: 40817812. DOI: 10.1093/jhered/esaf055.

Elaphodus cephalophus (tufted deer) :

1991

Shi, L., Yang, F., Kumamoto, A. :

The chromosomes of tufted deer (Elaphodus cephalophus). Cytogenet Cell Genet 56:189-92, 1991. Pubmed reference: 2055116. DOI: 10.1159/000133085.

Electrophorus electricus (electric eel) :

2025

Qi, Z., Liu, Q., Li, H., Zhang, Y., Yu, Z., Luo, W., Wang, K., Zhang, Y., Pan, S., Wang, C., Jiang, H., Qiu, Q., Wang, W., Fan, G., Li, Y. :

Telomere-to-telomere genome assembly of Electrophorus electricus provides insights into the evolution of electric eels. Gigascience 14:giaf024, 2025. Pubmed reference: 40167991. DOI: 10.1093/gigascience/giaf024.

Electrophorus voltai (Volta's electric eel) :

2025

Wang, Y., Liu, Y., Yang, Y., Bian, C., Liu, C., Zhang, Y., Mu, X. :

A chromosome-level genome assembly of Electrophorus voltai, a species of electric eel. Sci Data 12:1367, 2025. Pubmed reference: 40769985. DOI: 10.1038/s41597-025-05720-3.

Elephantidae (elephants) :

2003

Yang, F., Alkalaeva, E.Z., Perelman, P.L., Pardini, A.T., Harrison, W.R., O'Brien, P.C., Fu, B., Graphodatsky, A.S., Ferguson-Smith, M.A., Robinson, T.J. :

Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci U S A 100:1062-6, 2003. Pubmed reference: 12552116. DOI: 10.1073/pnas.0335540100.

Frönicke, L., Wienberg, J., Stone, G., Adams, L., Stanyon, R. :

Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting. Proc Biol Sci 270:1331-40, 2003. Pubmed reference: 12965023. DOI: 10.1098/rspb.2003.2383.

Elephas maximus (Asiatic elephant) :

2024

Shi, M., Chen, F., Sahu, S.K., Wang, Q., Yang, S., Wang, Z., Chen, J., Liu, H., Hou, Z., Fang, S.G., Lan, T. :

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 11:63, 2024. Pubmed reference: 38212399. DOI: 10.1038/s41597-023-02729-4.

2023

Cernohorska, H., Kubickova, S., Musilova, P., Vozdova, M., Vodicka, R., Rubes, J. :

Supernumerary Marker Chromosome Identified in Asian Elephant (Elephas maximus). Animals (Basel) 13:701, 2023. Pubmed reference: 36830488. DOI: 10.3390/ani13040701.

Prado, N.A., Armstrong, E.E., Brown, J.L., Goldenberg, S.Z., Leimgruber, P., Pearson, V.R., Maldonado, J.E., Campana, M.G. :

Genomic resources for Asian (Elephas maximus) and African Savannah elephant (Loxodonta africana) conservation and health research. J Hered 114:529-538, 2023. Pubmed reference: 37246890. DOI: 10.1093/jhered/esad034.

Li, X., Wang, P., Pan, Q., Liu, G., Liu, W., Omotoso, O., Du, J., Li, Z., Yu, Y., Huang, Y., Zhu, P., Li, M., Zhou, X. :

Chromosome-level Asian elephant genome assembly and comparative genomics of long-lived mammals reveal the common substitutions for cancer resistance. Aging Cell 22:e13917, 2023. Pubmed reference: 37395176. DOI: 10.1111/acel.13917.

1990

Sakthikumar, A., Mukundan, G., Raghunandanan, K.V. :

Chromosome Profile of Indian Elephants (Elephas-Maximus- Indicus). Indian Journal of Animal Sciences 60:175-182, 1990.

Eleutheronema tetradactylum (Indian salmon) :

2025

Zhang, H., Pan, Y., Miao, B., Wang, L., Zheng, A., Jin, M., Zhang, J., Tang, B., Wang, B., Huang, J., Li, J., Chong, D.H., Wang, Z. :

Near telomere-to-telomere genome assembly of the fourfinger threadfin (Eleutheronema tetradactylum). Sci Data , 2025. Pubmed reference: 41330960. DOI: 10.1038/s41597-025-06352-3.

Eliomys quercinus (garden dormouse) :

2024

Byerly, P.A., von Thaden, A., Leushkin, E., Hilgers, L., Liu, S., Winter, S., Schell, T., Gerheim, C., Ben Hamadou, A., Greve, C., Betz, C., Bolz, H.J., Büchner, S., Lang, J., Meinig, H., Famira-Parcsetich, E.M., Stubbe, S.P., Mouton, A., Bertolino, S., Verbeylen, G., Briner, T., Freixas, L., Vinciguerra, L., Mueller, S.A., Nowak, C., Hiller, M. :

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe. Genome Res 34:2094-2107, 2024. Pubmed reference: 39542649. DOI: 10.1101/gr.279066.124.

Elopichthys bambusa (yellowcheek carp) :

2024

Li, S., Xiong, X., Qiu, S., Shen, Z., He, Y., Gao, Z., Wan, S. :

Chromosome-level genome assembly of the yellow-cheek carp Elopichthys bambusa. Sci Data 11:426, 2024. Pubmed reference: 38658574. DOI: 10.1038/s41597-024-03262-8.

Embiotoca jacksoni (black perch) :

2022

Bernardi, G., Toy, J.A., Escalona, M., Marimuthu, M.P.A., Sahasrabudhe, R., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Miller, C., Shaffer, H.B. :

Reference genome of the black surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California kelp forest fish that lacks a pelagic larval stage. J Hered 113:657-664, 2022. Pubmed reference: 35809222. DOI: 10.1093/jhered/esac034.

Engraulis japonicus (Japanese anchovy) :

2025

Liu, S., Wang, L., Wang, R., Wang, H., Li, A., An, C., Meng, Z., Zhuang, Z. :

Chromosome-level genome assembly and annotation of Japanese anchovy (Engraulis japonicus). Sci Data 12:134, 2025. Pubmed reference: 39843454. DOI: 10.1038/s41597-025-04423-z.

Enhydra lutris (sea otter) :

2019

Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :

Aquatic adaptation and depleted diversity: A deep dive into the genomes of the sea otter and giant otter. Mol Biol Evol 36:2631-2655, 2019. Pubmed reference: 31212313. DOI: 10.1093/molbev/msz101.

2017

Jones, S.J., Haulena, M., Taylor, G.A., Chan, S., Bilobram, S., Warren, R.L., Hammond, S.A., Mungall, K.L., Choo, C., Kirk, H., Pandoh, P., Ally, A., Dhalla, N., Tam, A.K.Y., Troussard, A., Paulino, D., Coope, R.J.N., Mungall, A.J., Moore, R., Zhao, Y., Birol, I., Ma, Y., Marra, M., Jones, S.J.M. :

The genome of the Northern sea otter (Enhydra lutris kenyoni). Genes (Basel) 8:379, 2017. Pubmed reference: 29232880. DOI: 10.3390/genes8120379.

Entelurus aequoreus (snake pipefish) :

None

[No authors listed] :

GigaByte 2024:gigabyte105, None. Pubmed reference: 38239770. DOI: 10.46471/gigabyte.105.

Eolophus roseicapillus (galah) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Epinephelus awoara (yellow grouper) :

2024

Zhang, W., Yang, Y., Hua, S., Ruan, Q., Li, D., Wang, L., Wang, X., Wen, X., Liu, X., Meng, Z. :

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 11:151, 2024. Pubmed reference: 38296995. DOI: 10.1038/s41597-024-02989-8.

Epinephelus coioides (orange-spotted grouper) :

2025

Khalifa, R., Bean, T., Albatesh, D., van Aerle, R., Kahtir, Z., Hizam, Z., Gut, M., Câmara, F., Cruz, F., Gómez-Garrido, J., Alioto, T., Santos, E., Leitão, A., Minardi, D. :

Chromosome-level genome assembly of the hamour (orange-spotted grouper), Epinephelus coioides. F1000Res 14:1180, 2025. Pubmed reference: 41312210. DOI: 10.12688/f1000research.153918.1.

Epinephelus fuscoguttatus x Epinephelus polyphekadion (ShanHu grouper) :

2025

Liu, Y., Mao, Y. :

Chromosome-level genome assembly and genomic analysis of the hybrid grouper ShanHu (Epinephelus fuscoguttatus< ♀ × Epinephelus polyphekadion ♂). Int J Mol Sci 26:5036, 2025. Pubmed reference: 40507846. DOI: 10.3390/ijms26115036.

Epinephelus lanceolatus (giant grouper) :

2024

Zhou, Q., Liu, X., Song, Y., Li, M., Fan, G., Chen, S. :

Telomere-to-telomere gapless genome assembly of the giant grouper (Epinephelus lanceolatus). Sci Data 11:1342, 2024. Pubmed reference: 39695150. DOI: 10.1038/s41597-024-04219-7.

Epinephelus polyphekadion :

2024

Li, H., Liu, Y., Mao, M., Mao, Y. :

Chromosome-level genome assembly and annotation of the camouflage grouper (Epinephelus polyphekadion). Sci Data 11:1353, 2024. Pubmed reference: 39695304. DOI: 10.1038/s41597-024-04212-0.

Equus asinus (ass (donkey)) :

2025

Du, W., Sun, Q., Hu, S., Yu, P., Kan, S., Zhang, W. :

Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses. Sci Rep 15:6803, 2025. Pubmed reference: 40000832. DOI: 10.1038/s41598-025-91564-1.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Yang, G., Gong, M., Yang, Q.M., Li, Y.D., Halima, J., Lei, C.Z., Jiang, Y., Dang, R.H. :

Improved chromosome-level donkey (Equus asinus) genome provides insights into genome and chromosome evolution. J Genet Genomics 52:269-272, 2024. Pubmed reference: 39542171. DOI: 10.1016/j.jgg.2024.11.002.

2023

Duhan, N., Kaur, S., Kaundal, R. :

Jevit, M.J., Castaneda, C., Paria, N., Das, P.J., Miller, D., Antczak, D.F., Kalbfleisch, T.S., Davis, B.W., Raudsepp, T. :

Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 13:20180, 2023. Pubmed reference: 37978222. DOI: 10.1038/s41598-023-47583-x.

2022

Miao, X., Yu, Y., Zhao, Z., Wang, Y., Qian, X., Wang, Y., Li, S., Wang, C. :

Chromosome-level haplotype assembly for Equus asinu. Front Genet 13:738105, 2022. Pubmed reference: 35692816. DOI: 10.3389/fgene.2022.738105.

2021

Wang, Y., Miao, X., Zhao, Z., Wang, Y., Li, S., Wang, C. :

Transcriptome atlas of 16 donkey tissues. Front Genet 12:682734, 2021. Pubmed reference: 34434218. DOI: 10.3389/fgene.2021.682734.

2020

Wang, C., Li, H., Guo, Y., Huang, J., Sun, Y., Min, J., Wang, J., Fang, X., Zhao, Z., Wang, S., Zhang, Y., Liu, Q., Jiang, Q., Wang, X., Guo, Y., Yang, C., Wang, Y., Tian, F., Zhuang, G., Fan, Y., Gao, Q., Li, Y., Ju, Z., Li, J., Li, R., Hou, M., Yang, G., Liu, G., Liu, W., Guo, J., Pan, S., Fan, G., Zhang, W., Zhang, R., Yu, J., Zhang, X., Yin, Q., Ji, C., Jin, Y., Yue, G., Liu, M., Xu, J., Liu, S., Jordana, J., Noce, A., Amills, M., Wu, D.D., Li, S., Zhou, X., Zhong, J. :

Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 11:6014, 2020. Pubmed reference: 33293529. DOI: 10.1038/s41467-020-19813-7.

2016

Sun, Y., Jiang, Q., Yang, C., Wang, X., Tian, F., Wang, Y., Ma, Y., Ju, Z., Huang, J., Zhou, X., Zhong, J., Wang, C. :

Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis. Curr Genet 62:383-90, 2016. Pubmed reference: 26527116. DOI: 10.1007/s00294-015-0531-9.

2015

Bertolini, F., Scimone, C., Geraci, C., Schiavo, G., Utzeri, V.J., Chiofalo, V., Fontanesi, L. :

Next generation semiconductor based sequencing of the donkey (Equus asinus) genome provided comparative sequence data against the horse genome and a few millions of single nucleotide polymorphisms. PLoS One 10:e0131925, 2015. Pubmed reference: 26151450. DOI: 10.1371/journal.pone.0131925.

2009

Di Meo, G.P., Perucatti, A., Peretti, V., Incarnato, D., Ciotola, F., Liotta, L., Raudsepp, T., Di Berardino, D., Chowdhary, B., Iannuzzi, L. :

The 450-band resolution G- and R-banded standard karyotype of the donkey (Equus asinus, 2n = 62). Cytogenet Genome Res 125:266-71, 2009. Pubmed reference: 19864889. DOI: 10.1159/000235932.

2000

Raudsepp, T., Christensen, K., Chowdhar, B.P. :

Cytogenetics of donkey chromosomes: nomenclature proposal based on GTG-banded chromosomes and depiction of NORs and telomeric sites. Chromosome Res 8:659-70, 2000. Pubmed reference: 11196129. DOI: 10.1023/a:1026707002538.

1996

Xu, X., Gullberg, A., Arnason, U. :

The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. J Mol Evol 43:438-46, 1996. Pubmed reference: 8875857. DOI: 10.1007/BF02337515.

1992

Vijh, R.K., Sahai, R., Sharma, A. :

Chromosomes of Indian Domestic Donkey (Equus Asinus). Indian Journal of Animal Sciences 62:1103-1106, 1992.

1990

Ryder, O.A., Chemnick, L.G. :

Chromosomal and molecular evolution in Asiatic wild asses. Genetica 83:67-72, 1990. Pubmed reference: 2090563. DOI: 10.1007/BF00774690.

1976

Eldridge, F., Blazak, W.F. :

Horse, ass, and mule chromosomes. J Hered 67:361-7, 1976. Pubmed reference: 1021594. DOI: 10.1093/oxfordjournals.jhered.a108753.

1974

Chandley, A.C., Jones, R.C., Dott, H.M., Allen, W.R., Short, R.V. :

Meiosis in interspecific equine hybrids. I. The male mule (Equus asinus X E. caballus) and hinny (E. caballus X E. asinus). Cytogenet Cell Genet 13:330-41, 1974. Pubmed reference: 4430187. DOI: 10.1159/000130284.

Equus asinus x Equus caballus (mule) :

1976

Eldridge, F., Blazak, W.F. :

Horse, ass, and mule chromosomes. J Hered 67:361-7, 1976. Pubmed reference: 1021594. DOI: 10.1093/oxfordjournals.jhered.a108753.

Eldridge, F., Suzuki, Y. :

A mare mule--dam or foster mother? J Hered 67:353-60, 1976. Pubmed reference: 1035593. DOI: 10.1093/oxfordjournals.jhered.a108752.

Equus caballus (domestic horse) :

2025

Sharma, N.K., Singh, P., Saha, B., Bhardwaj, A., Iquebal, M.A., Pal, Y., Nayan, V., Jaiswal, S., Giri, S.K., Legha, R.A., Bhattacharya, T.K., Kumar, D., Rai, A. :

Genome wide landscaping of copy number variations for horse inter-breed variability. Anim Biotechnol 36:2446251, 2025. Pubmed reference: 39791493. DOI: 10.1080/10495398.2024.2446251.

Du, W., Sun, Q., Hu, S., Yu, P., Kan, S., Zhang, W. :

Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses. Sci Rep 15:6803, 2025. Pubmed reference: 40000832. DOI: 10.1038/s41598-025-91564-1.

Li, X., Wang, Z., Zhu, M., Wang, B., Teng, S., Yan, J., Wang, H., Yuan, P., Cao, S., Qu, X., Wang, Z., Zhan, K., Choudhury, M.P., Yang, X., Bao, Q., He, S., Liu, L., Zhao, P., Jiang, J., Xiang, H., Fang, L., Tang, Z., Liao, Y., Yi, G. :

Genomic insights into post-domestication expansion and selection of body size in ponies. Adv Sci (Weinh) 12:e2413023, 2025. Pubmed reference: 40009528. DOI: 10.1002/advs.202413023.

Barber, A.M., Kingsley, N.B., Peng, S., Giulotto, E., Bellone, R.R., Finno, C.J., Kalbfleisch, T., Petersen, J.L. :

Annotation of cis-regulatory-associated histone modifications in the genomes of two Thoroughbred stallions. Front Genet 16:1534461, 2025. Pubmed reference: 40084169. DOI: 10.3389/fgene.2025.1534461.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Steensma, M.J., Ducro, B.J., Dibbits, B., Doekes, H.P., van Schipstal, J.G.C., Kalblfleisch, T., Groenen, M.A.M., Derks, M.F.L. :

High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning. BMC Genomics 26:790, 2025. Pubmed reference: 40890628. DOI: 10.1186/s12864-025-11985-0.

Cullen, J.N., Cieslak, J., Petersen, J.L., Bellone, R.R., Finno, C.J., Kalbfleisch, T.S., Calloe, K., Capomaccio, S., Cappelli, K., Coleman, S.J., Distl, O., Durward-Akhurst, S.A., Giulotto, E., Hamilton, N.A., Hill, E.W., Katz, L.M., Klaerke, D.A., Lindgren, G., MacHugh, D.E., Mackowski, M., MacLeod, J.N., Metzger, J., Murphy, B.A., Orlando, L., Raudsepp, T., Silvestrelli, M., Strand, E., Tozaki, T., Trachsel, D.S., Valderrama Figueroa, L.S., Velie, B.D., Wade, C.M., Waud, B., Mickelson, J.R., McCue, M.E. :

Charting the equine miRNA landscape: An integrated pipeline and browser for annotating, quantifying, and visualizing expression. PLoS Genet 21:e1011835, 2025. Pubmed reference: 40911641. DOI: 10.1371/journal.pgen.1011835.

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Pokharel, K., Weldenegodguad, M., Reilas, T., Kantanen, J. :

EquCab_Finn: A new reference genome assembly for the domestic horse, Finnhorse. Anim Genet 55:766-771, 2024. Pubmed reference: 38986537. DOI: 10.1111/age.13463.

Bailey, E., Finno, C.J., Cullen, J.N., Kalbfleisch, T., Petersen, J.L. :

Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations. Sci Rep 14:22930, 2024. Pubmed reference: 39358442. DOI: 10.1038/s41598-024-73645-9.

Ahlawat, S., Niranjan, S.K., Arora, R., Vijh, R.K., Kumar, A., Sharma, U., Raheja, M., Popli, K., Yadav, S., Mehta, S.C. :

Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies. Funct Integr Genomics 24:195, 2024. Pubmed reference: 39441226. DOI: 10.1007/s10142-024-01482-0.

Assanbayev, T., Akilzhanov, R., Sharapatov, T., Bektayev, R., Samatkyzy, D., Karabayev, D., Gabdulkayum, A., Daniyarov, A., Rakhimova, S., Kozhamkulov, U., Sarbassov, D., Akilzhanova, A., Kairov, U. :

Whole genome sequencing and de novo genome assembly of the Kazakh native horse Zhabe. Front Genet 15:1466382, 2024. Pubmed reference: 39529846. DOI: 10.3389/fgene.2024.1466382.

2023

Peng, S., Dahlgren, A.R., Donnelly, C.G., Hales, E.N., Petersen, J.L., Bellone, R.R., Kalbfleisch, T., Finno, C.J. :

Functional annotation of the animal genomes: An integrated annotation resource for the horse. PLoS Genet 19:e1010468, 2023. Pubmed reference: 36862752. DOI: 10.1371/journal.pgen.1010468.

Tozaki, T., Ohnuma, A., Kikuchi, M., Ishige, T., Kakoi, H., Hirota, K.I., Takahashi, Y., Nagata, S.I. :

Short insertion and deletion discoveries via whole-genome sequencing of 101 Thoroughbred racehorses. Genes (Basel) 14:638, 2023. Pubmed reference: 36980910. DOI: 10.3390/genes14030638.

Gu, J., Li, S., Zhu, B., Liang, Q., Chen, B., Tang, X., Chen, C., Wu, D.D., Li, Y. :

Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Mol Ecol Resour 23:1656-1672, 2023. Pubmed reference: 37259205. DOI: 10.1111/1755-0998.13818.

Tozaki, T., Ohnuma, A., Kikuchi, M., Ishige, T., Kakoi, H., Hirora, K.I., Nagata, S.I. :

Use of whole-genome variants and their frequency data to estimate haplotype structure in the Thoroughbred genome. Anim Genet 54:662-663, 2023. Pubmed reference: 37336519. DOI: 10.1111/age.13338.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Vasoya, D., Tzelos, T., Benedictus, L., Karagianni, A.E., Pirie, S., Marr, C., Oddsdóttir, C., Fintl, C., Connelley, T. :

High-resolution genotyping of expressed equine MHC reveals a highly complex MHC structure. Genes (Basel) 14:1422, 2023. Pubmed reference: 37510326. DOI: 10.3390/genes14071422.

Duhan, N., Kaur, S., Kaundal, R. :

Cappelletti, E., Piras, F.M., Sola, L., Santagostino, M., Petersen, J.L., Bellone, R.R., Finno, C.J., Peng, S., Kalbfleisch, T.S., Bailey, E., Nergadze, S.G., Giulotto, E. :

The localization of centromere protein A is conserved among tissues. Commun Biol 6:963, 2023. Pubmed reference: 37735603. DOI: 10.1038/s42003-023-05335-7.

Jevit, M.J., Castaneda, C., Paria, N., Das, P.J., Miller, D., Antczak, D.F., Kalbfleisch, T.S., Davis, B.W., Raudsepp, T. :

Tang, X., Zhu, B., Ren, R., Chen, B., Li, S., Gu, J. :

Genome-wide copy number variation detection in a large cohort of diverse horse breeds by whole-genome sequencing. Front Vet Sci 10:1296213, 2023. Pubmed reference: 38076560. DOI: 10.3389/fvets.2023.1296213.

2021

Peng, S., Petersen, J.L., Bellone, R.R., Kalbfleisch, T., Kingsley, N.B., Barber, A.M., Cappelletti, E., Giulotto, E., Finno, C.J. :

Decoding the equine genome: Lessons from ENCODE. Genes (Basel) 12:1707, 2021. Pubmed reference: 34828313. DOI: 10.3390/genes12111707.

Durward-Akhurst, S.A., Schaefer, R.J., Grantham, B., Carey, W.K., Mickelson, J.R., McCue, M.E. :

Genetic variation and the distribution of variant types in the horse. Front Genet 12:758366, 2021. Pubmed reference: 34925451. DOI: 10.3389/fgene.2021.758366.

2020

Beeson, S.K., Mickelson, J.R., McCue, M.E. :

Equine recombination map updated to EquCab3.0. Anim Genet 51:341-2, 2020. Pubmed reference: 31887785. DOI: 10.1111/age.12898.

Schaefer, R.J., McCue, M.E. :

Equine genotyping arrays. Vet Clin North Am Equine Pract 36:183-93, 2020. Pubmed reference: 32534852. DOI: 10.1016/j.cveq.2020.03.001.

2018

Janečka, J.E., Davis, B.W., Ghosh, S., Paria, N., Das, P.J., Orlando, L., Schubert, M., Nielsen, M.K., Stout, T.A.E., Brashear, W., Li, G., Johnson, C.D., Metz, R.P., Zadjali, A.M.A., Love, C.C., Varner, D.D., Bellott, D.W., Murphy, W.J., Chowdhary, B.P., Raudsepp, T. :

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun 9:2945, 2018. Pubmed reference: 30054462. DOI: 10.1038/s41467-018-05290-6.

Kalbfleisch, T.S., Rice, E.S., DePriest, M.S., Walenz, B.P., Hestand, M.S., Vermeesch, J.R., O Connell, B.L., Fiddes, I.T., Vershinina, A.O., Saremi, N.F., Petersen, J.L., Finno, C.J., Bellone, R.R., McCue, M.E., Brooks, S.A., Bailey, E., Orlando, L., Green, R.E., Miller, D.C., Antczak, D.F., MacLeod, J.N. :

Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 1:197, 2018. Pubmed reference: 30456315. DOI: 10.1038/s42003-018-0199-z.

2017

Schaefer, R.J., Schubert, M., Bailey, E., Bannasch, D.L., Barrey, E., Bar-Gal, G.K., Brem, G., Brooks, S.A., Distl, O., Fries, R., Finno, C.J., Gerber, V., Haase, B., Jagannathan, V., Kalbfleisch, T., Leeb, T., Lindgren, G., Lopes, M.S., Mach, N., da Câmara Machado, A., MacLeod, J.N., McCoy, A., Metzger, J., Penedo, C., Polani, S., Rieder, S., Tammen, I., Tetens, J., Thaller, G., Verini-Supplizi, A., Wade, C.M., Wallner, B., Orlando, L., Mickelson, J.R., McCue, M.E. :

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 18:565, 2017. Pubmed reference: 28750625. DOI: 10.1186/s12864-017-3943-8.

2013

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., Johnson, P.L., Fumagalli, M., Vilstrup, J.T., Raghavan, M., Korneliussen, T., Malaspinas, A.S., Vogt, J., Szklarczyk, D., Kelstrup, C.D., Vinther, J., Dolocan, A., Stenderup, J., Velazquez, A.M., Cahill, J., Rasmussen, M., Wang, X., Min, J., Zazula, G.D., Seguin-Orlando, A., Mortensen, C., Magnussen, K., Thompson, J.F., Weinstock, J., Gregersen, K., Røed, K.H., Eisenmann, V., Rubin, C.J., Miller, D.C., Antczak, D.F., Bertelsen, M.F., Brunak, S., Al-Rasheid, K.A., Ryder, O., Andersson, L., Mundy, J., Krogh, A., Gilbert, M.T., Kjær, K., Sicheritz-Ponten, T., Jensen, L.J., Olsen, J.V., Hofreiter, M., Nielsen, R., Shapiro, B., Wang, J., Willerslev, E. :

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499:74-8, 2013. Pubmed reference: 23803765. DOI: 10.1038/nature12323.

2012

McCue, M.E., Bannasch, D.L., Petersen, J.L., Gurr, J., Bailey, E., Binns, M.M., Distl, O., Guérin, G., Hasegawa, T., Hill, E.W., Leeb, T., Lindgren, G., Penedo, M.C., Røed, K.H., Ryder, O.A., Swinburne, J.E., Tozaki, T., Valberg, S.J., Vaudin, M., Lindblad-Toh, K., Wade, C.M., Mickelson, J.R. :

A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 8:e1002451, 2012. Pubmed reference: 22253606. DOI: 10.1371/journal.pgen.1002451.

2010

Mittmann, E.H., Wrede, J., Pook, J., Distl, O. :

Identification of 21 781 equine microsatellites on the horse genome assembly 2.0. Anim Genet 41:222, 2010. Pubmed reference: 19793266. DOI: 10.1111/j.1365-2052.2009.01970.x.

2009

Wade, C.M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., Lear, T.L., Adelson, D.L., Bailey, E., Bellone, R.R., Blöcker, H., Distl, O., Edgar, R.C., Garber, M., Leeb, T., Mauceli, E., MacLeod, J.N., Penedo, M.C., Raison, J.M., Sharpe, T., Vogel, J., Andersson, L., Antczak, D.F., Biagi, T., Binns, M.M., Chowdhary, B.P., Coleman, S.J., Della Valle, G., Fryc, S., Guérin, G., Hasegawa, T., Hill, E.W., Jurka, J., Kiialainen, A., Lindgren, G., Liu, J., Magnani, E., Mickelson, J.R., Murray, J., Nergadze, S.G., Onofrio, R., Pedroni, S., Piras, M.F., Raudsepp, T., Rocchi, M., Røed, K.H., Ryder, O.A., Searle, S., Skow, L., Swinburne, J.E., Syvänen, A.C., Tozaki, T., Valberg, S.J., Vaudin, M., White, J.R., Zody, M.C. :

Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865-7, 2009. Pubmed reference: 19892987. DOI: 10.1126/science.1178158.

2008

Raudsepp, T., Gustafson-Seabury, A., Durkin, K., Wagner, M.L., Goh, G., Seabury, C.M., Brinkmeyer-Langford, C., Lee, E.J., Agarwala, R., Stallknecht-Rice, E., Schäffer, A.A., Skow, L.C., Tozaki, T., Yasue, H., Penedo, M.C., Lyons, L.A., Khazanehdari, K.A., Binns, M.M., MacLeod, J.N., Distl, O., Guérin, G., Leeb, T., Mickelson, J.R., Chowdhary, B.P. :

A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenet Genome Res 122:28-36, 2008. Pubmed reference: 18931483. DOI: 10.1159/000151313.

Chowdhary, B.P., Raudsepp, T. :

The horse genome derby: racing from map to whole genome sequence. Chromosome Res 16:109-27, 2008. Pubmed reference: 18274866. DOI: 10.1007/s10577-008-1204-z.

Brinkmeyer-Langford, C., Raudsepp, T., Gustafson-Seabury, A., Chowdhary, B.P. :

A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet Genome Res 120:164-72, 2008. Pubmed reference: 18467843. DOI: 10.1159/000118758.

2007

Tozaki, T., Swinburne, J., Hirota, K., Hasegawa, T., Ishida, N., Tobe, T. :

Improved resolution of the comparative horse-human map: investigating markers with in silico and linkage mapping approaches. Gene 392:181-6, 2007. Pubmed reference: 17306472. DOI: 10.1016/j.gene.2006.12.018.

Goh, G., Raudsepp, T., Durkin, K., Wagner, M.L., Schäffer, A.A., Agarwala, R., Tozaki, T., Mickelson, J.R., Chowdhary, B.P. :

High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals. Genomics 89:89-112, 2007. Pubmed reference: 16916595. DOI: 10.1016/j.ygeno.2006.06.012.

2006

Dierks, C., Mömke, S., Drögemüller, C., Leeb, T., Chowdhary, B.P., Distl, O. :

A high-resolution comparative radiation hybrid map of equine chromosome 4q12-q22. Anim Genet 37:513-7, 2006. Pubmed reference: 16978184. DOI: 10.1111/j.1365-2052.2006.01510.x.

Chowdhary, B.P., Raudsepp, T. :

The horse genome. Genome Dyn 2:97-110, 2006. Pubmed reference: 18753773. DOI: 10.1159/000095098.

Leeb, T., Vogl, C., Zhu, B., de Jong, P.J., Binns, M.M., Chowdhary, B.P., Scharfe, M., Jarek, M., Nordsiek, G., Schrader, F., Blöcker, H. :

A human-horse comparative map based on equine BAC end sequences. Genomics 87:772-6, 2006. Pubmed reference: 16603334. DOI: 10.1016/j.ygeno.2006.03.002.

Perrocheau, M., Boutreux, V., Chadi, S., Mata, X., Decaunes, P., Raudsepp, T., Durkin, K., Incarnato, D., Iannuzzi, L., Lear, T.L., Hirota, K., Hasegawa, T., Zhu, B., de Jong, P., Cribiu, E.P., Chowdhary, B.P., Guérin, G. :

Construction of a medium-density horse gene map. Anim Genet 37:145-55, 2006. Pubmed reference: 16573529. DOI: 10.1111/j.1365-2052.2005.01401.x.

Wagner, M.L., Raudsepp, T., Goh, G., Agarwala, R., Schaffer, A.A., Dranchak, P.K., Brinkmeyer-Langford, C., Skow, L.C., Chowdhary, B.P., Mickelson, J.R. :

A 1.3-Mb interval map of equine homologs of HSA2. Cytogenet Genome Res 112:227-34, 2006. Pubmed reference: 16484777. DOI: 10.1159/000089875.

Swinburne, J.E., Boursnell, M., Hill, G., Pettitt, L., Allen, T., Chowdhary, B., Hasegawa, T., Kurosawa, M., Leeb, T., Mashima, S., Mickelson, J.R., Raudsepp, T., Tozaki, T., Binns, M. :

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families. Genomics 87:1-29, 2006. Pubmed reference: 16314071. DOI: 10.1016/j.ygeno.2005.09.001.

2005

Brinkmeyer-Langford, C., Raudsepp, T., Lee, E.J., Goh, G., Schäffer, A.A., Agarwala, R., Wagner, M.L., Tozaki, T., Skow, L.C., Womack, J.E., Mickelson, J.R., Chowdhary, B.P. :

A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 16:631-49, 2005. Pubmed reference: 16180145. DOI: 10.1007/s00335-005-0023-1.

Penedo, M.C., Millon, L.V., Bernoco, D., Bailey, E., Binns, M., Cholewinski, G., Ellis, N., Flynn, J., Gralak, B., Guthrie, A., Hasegawa, T., Lindgren, G., Lyons, L.A., Røed, K.H., Swinburne, J.E., Tozaki, T. :

International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenet Genome Res 111:5-15, 2005. Pubmed reference: 16093715. DOI: 10.1159/000085664.

Gustafson-Seabury, A., Raudsepp, T., Goh, G., Kata, S.R., Wagner, M.L., Tozaki, T., Mickelson, J.R., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

High-resolution RH map of horse chromosome 22 reveals a putative ancestral vertebrate chromosome. Genomics 85:188-200, 2005. Pubmed reference: 15676277. DOI: 10.1016/j.ygeno.2004.10.012.

2004

Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Mickelson, J.R. :

Sixty-seven new equine microsatellite loci assigned to the equine radiation hybrid map. Anim Genet 35:484-6, 2004. Pubmed reference: 15566483. DOI: 10.1111/j.1365-2052.2004.01205.x.

Mickelson, J.R., Wagner, M.L., Goh, G., Wu, J.T., Morrison, L.Y., Alexander, L.J., Raudsepp, T., Skow, L.C., Chowdhary, B.P., Swinburne, J.E., Binns, M.M. :

Thirty-five new equine microsatellite loci assigned to genetic linkage and radiation hybrid maps. Anim Genet 35:481-4, 2004. Pubmed reference: 15566482. DOI: 10.1111/j.1365-2052.2004.01206.x.

Raudsepp, T., Santani, A., Wallner, B., Kata, S.R., Ren, C., Zhang, H.B., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

A detailed physical map of the horse Y chromosome. Proc Natl Acad Sci U S A 101:9321-6, 2004. Pubmed reference: 15197257. DOI: 10.1073/pnas.0403011101.

Yang, F., Fu, B., O'Brien, P.C., Nie, W., Ryder, O.A., Ferguson-Smith, M.A. :

Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules. Chromosome Res 12:65-76, 2004. Pubmed reference: 14984103. DOI: 10.1023/b:chro.0000009298.02689.8a.

Lee, E.J., Raudsepp, T., Kata, S.R., Adelson, D., Womack, J.E., Skow, L.C., Chowdhary, B.P. :

A 1.4-Mb interval RH map of horse chromosome 17 provides detailed comparison with human and mouse homologues. Genomics 83:203-15, 2004. Pubmed reference: 14706449. DOI: 10.1016/j.ygeno.2003.07.002.

2003

Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Biros, I., Bjørnstad, G., Bowling, A.T., Brandon, R., Caetano, A.R., Cholewinski, G., Colling, D., Eggleston, M., Ellis, N., Flynn, J., Gralak, B., Hasegawa, T., Ketchum, M., Lindgren, G., Lyons, L.A., Millon, L.V., Mariat, D., Murray, J., Neau, A., Røed, K., Sandberg, K., Skow, L.C., Tammen, I., Tozaki, T., Van Dyk, E., Weiss, B., Young, A., Ziegle, J. :

The second generation of the International Equine Gene Mapping Workshop half-sibling linkage map. Anim Genet 34:161-8, 2003. Pubmed reference: 12755815. DOI: 10.1046/j.1365-2052.2003.00973.x.

Chowdhary, B.P., Raudsepp, T., Kata, S.R., Goh, G., Millon, L.V., Allan, V., Piumi, F., Guérin, G., Swinburne, J., Binns, M., Lear, T.L., Mickelson, J., Murray, J., Antczak, D.F., Womack, J.E., Skow, L.C. :

The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res 13:742-51, 2003. Pubmed reference: 12671008. DOI: 10.1101/gr.917503.

Swinburne, J.E., Turner, A., Alexander, L.J., Mickleson, J.R., Binns, M.M. :

Characterization and linkage map assignments for 61 new horse microsatellite loci (AHT49-109). Anim Genet 34:65-8, 2003. Pubmed reference: 12580791. DOI: 10.1046/j.1365-2052.2003.00951_1.x.

Yang, F., Fu, B., O'Brien, P.C., Robinson, T.J., Ryder, O.A., Ferguson-Smith, M.A. :

Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet Genome Res 102:235-43, 2003. Pubmed reference: 14970709. DOI: 10.1159/000075755.

2002

O'Rourke, K. :

And coming around the track, looking promising ... the horse genome map. J Am Vet Med Assoc 221:15, 20, 2002. Pubmed reference: 12420810.

Chowdhary, B.P., Raudsepp, T., Honeycutt, D., Owens, E.K., Piumi, F., Guérin, G., Matise, T.C., Kata, S.R., Womack, J.E., Skow, L.C. :

Construction of a 5000(rad) whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11. Mamm Genome 13:89-94, 2002. Pubmed reference: 11889556. DOI: 10.1007/s00335-001-2089-8.

2001

Lear, T.L., Brandon, R., Piumi, F., Terry, R.R., Guérin, G., Thomas, S., Bailey, E. :

Mapping of 31 horse genes in BACs by FISH. Chromosome Res 9:261-2, 2001. Pubmed reference: 11330401. DOI: 10.1023/a:1016608806205.

2000

Kiguwa, S.L., Hextall, P., Smith, A.L., Critcher, R., Swinburne, J., Millon, L., Binns, M.M., Goodfellow, P.N., McCarthy, L.C., Farr, C.J., Oakenfull, E.A. :

A horse whole-genome-radiation hybrid panel: chromosome 1 and 10 preliminary maps. Mamm Genome 11:803-5, 2000. Pubmed reference: 10967144. DOI: 10.1007/s003350010146.

Swinburne, J., Gerstenberg, C., Breen, M., Aldridge, V., Lockhart, L., Marti, E., Antczak, D., Eggleston-Stott, M., Bailey, E., Mickelson, J., Røed, K., Lindgren, G., von Haeringen, W., Guérin, G., Bjarnason, J., Allen, T., Binns, M. :

First comprehensive low-density horse linkage map based on two 3-generation, full-sibling, cross-bred horse reference families. Genomics 66:123-34, 2000. Pubmed reference: 10860657. DOI: 10.1006/geno.2000.6207.

1999

Caetano, A.R., Shiue, Y.L., Lyons, L.A., O'Brien, S.J., Laughlin, T.F., Bowling, A.T., Murray, J.D. :

A comparative gene map of the horse (Equus caballus). Genome Res 9:1239-49, 1999. Pubmed reference: 10613847. DOI: 10.1101/gr.9.12.1239.

Guérin, G., Bailey, E., Bernoco, D., Anderson, I., Antczak, D.F., Bell, K., Binns, M.M., Bowling, A.T., Brandon, R., Cholewinski, G., Cothran, E.G., Ellegren, H., Förster, M., Godard, S., Horin, P., Ketchum, M., Lindgren, G., McPartlan, H., Mériaux, J.C., Mickelson, J.R., Millon, L.V., Murray, J., Neau, A., Røed, K., Ziegle, J. :

Report of the International Equine Gene Mapping Workshop: male linkage map. Anim Genet 30:341-54, 1999. Pubmed reference: 10582279. DOI: 10.1046/j.1365-2052.1999.00510.x.

Shiue, Y.L., Bickel, L.A., Caetano, A.R., Millon, L.V., Clark, R.S., Eggleston, M.L., Michelmore, R., Bailey, E., Guérin, G., Godard, S., Mickelson, J.R., Valberg, S.J., Murray, J.D., Bowling, A.T. :

A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. Anim Genet 30:1-9, 1999. Pubmed reference: 10050277. DOI: 10.1046/j.1365-2052.1999.00377.x.

1998

Bailey, E., Binns, M.M. :

The Horse Gene Map. ILAR J 39:171-176, 1998. Pubmed reference: 11528075. DOI: 10.1093/ilar.39.2-3.171.

Lindgren, G., Sandberg, K., Persson, H., Marklund, S., Breen, M., Sandgren, B., Carlstén, J., Ellegren, H. :

A primary male autosomal linkage map of the horse genome. Genome Res 8:951-66, 1998. Pubmed reference: 9750194. DOI: 10.1101/gr.8.9.951.

1997

Bowling, A.T., Breen, M., Chowdhary, B.P., Hirota, K., Lear, T., Millon, L.V., Ponce de Leon, F.A., Raudsepp, T., Stranzinger, G. :

International system for cytogenetic nomenclature of the domestic horse. Report of the Third International Committee for the Standardization of the domestic horse karyotype, Davis, CA, USA, 1996. Chromosome Res 5:433-43, 1997. Pubmed reference: 9421259. DOI: 10.1023/a:1018408811881.

1996

Bowling, A.T. :

Horse Genetics. (1st edn), CAB International, Wallingford , 1996.

1994

Ryder, O.A. :

A Horse of a Different Chromosome. Natural History 103:54, 1994.

1993

Rønne, M., Gyldenholm, A.O., Storm, C.O. :

The RBG-banded karyotype of Equus caballus at the 525-band stage. Hereditas 118:195-9, 1993. Pubmed reference: 8335476. DOI: 10.1111/j.1601-5223.1993.00195.x.

1992

Lear, T.L., Trembicki, K.A., Ennis, R.B. :

Identification of equine chromosomes in horse x mouse somatic cell hybrids. Cytogenet Cell Genet 61:58-60, 1992. Pubmed reference: 1505233. DOI: 10.1159/000133369.

1991

Morenomillan, M., Rodero, A., Alonso, F.J., Sanz, A. :

1st Report of Cytogenetic Studies in Spanish Breed Horses. Genetics Selection Evolution 23:S176-S178, 1991.

Vijh, R.K., Sahai, R., Sharma, A., Mahaney, N.K. :

Chromosomal Complement of the Indian Domestic Horse. Indian Journal of Animal Sciences 61:546-549, 1991.

1990

Richer, C.L., Power, M.M., Klunder, L.R., McFeely, R.A., Kent, M.G. :

Standard karyotype of the domestic horse (Equus caballus). Committee for standardized karyotype of Equus caballus. The Second International Conference for Standardization of Domestic Animal Karyotypes, INRA, Jouy-en Josas, France, 22nd-26th May 1989. Hereditas 112:289-93, 1990. Pubmed reference: 1976611. DOI: 10.1111/j.1601-5223.1990.tb00069.x.

King, W.A., Desjardins, M., Xu, K.P., Bousquet, D. :

Chromosome Analysis of Horse Oocytes Cultured Invitro. Genetics Selection Evolution 22:151-160, 1990.

Lui, J.F., Giannoni, M.A., Giannoni, M.L., Tosta, P.A. :

Characteristics of NOR-Banded Chromosomes of Mangalarga Horses. Revista Brasileira de Genetica 13:269-281, 1990.

1989

Romagnano, A., Richer, C.L. :

Cytogenetics of the Horse - Adult and Embryonic Cells. Cytogenetics of Animals, (ed. Halnan, C.R.E.) :159-183, 1989.

1987

Romagnano, A., Drouin, R., Richer, C.L. :

Idiograms of horse chromosomes at prometaphase, early metaphase, and midmetaphase after R-banding by BrdU incorporation followed by the fluorochrome-photolysis-Giemsa technique. Genome 29:674-9, 1987. Pubmed reference: 3666451. DOI: 10.1139/g87-113.

1985

Molteni, L., Cribiu, E.P., Macchi, A. de G., Beltrami, E., Succi, G. :

[Description of horse (Equus caballus) chromosomes after treatment with BrdU and staining with acridine orange]. Zootecnica e Nutrizione Animale 11:183-190, 1985.

1981

Kopp, E., Mayr, B., Czaker, R., Schleger, W. :

Nucleolus organizer regions in the chromosomes of the domestic horse. J Hered 72:357-8, 1981. Pubmed reference: 7328305. DOI: 10.1093/oxfordjournals.jhered.a109525.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1978

Ryder, O.A., Epel, N.C., Benirschke, K. :

Chromosome banding studies of the Equidae. Cytogenet Cell Genet 20:332-50, 1978. Pubmed reference: 648186.

1976

Eldridge, F., Blazak, W.F. :

Horse, ass, and mule chromosomes. J Hered 67:361-7, 1976. Pubmed reference: 1021594. DOI: 10.1093/oxfordjournals.jhered.a108753.

Buckland, R.A., Fletcher, J.M., Chandley, C. :

Characterization of the domestic horse (Equus caballus) karyotype using G- and C-banding techniques. Experientia 32:1146-9, 1976. Pubmed reference: 971746. DOI: 10.1007/BF01927593.

1974

Chandley, A.C., Jones, R.C., Dott, H.M., Allen, W.R., Short, R.V. :

Short, R.V., Chandley, A.C., Jones, R.C., Allen, W.R. :

Meiosis in interspecific equine hybrids. II. The przewalski horse/domestic horse hybrid. Cytogenet Cell Genet 13:465-78, 1974. Pubmed reference: 4462982. DOI: 10.1159/000130300.

1962

SASAKI, M.S., MAKINO, S. :

Revised study of the chromosomes of domestic cattle and the horse in somatic cells in vitro. J Hered 53:157-62, 1962. Pubmed reference: 13986625. DOI: 10.1093/oxfordjournals.jhered.a107156.

Equus grevyi (Grevy's zebra) :

2008

2007

Musilova, P., Kubickova, S., Zrnova, E., Horin, P., Vahala, J., Rubes, J. :

Karyotypic relationships among Equus grevyi, Equus burchelli and domestic horse defined using horse chromosome arm-specific probes. Chromosome Res 15:807-13, 2007. Pubmed reference: 17874215. DOI: 10.1007/s10577-007-1164-8.

Equus hemionus (onager) :

2009

Musilova, P., Kubickova, S., Horin, P., Vodicka, R., Rubes, J. :

Karyotypic relationships in Asiatic asses (kulan and kiang) as defined using horse chromosome arm-specific and region-specific probes. Chromosome Res 17:783-90, 2009. Pubmed reference: 19731053. DOI: 10.1007/s10577-009-9069-3.

2008

1978

Ryder, O.A. :

Chromosomal polymorphism in Equus hemionus. Cytogenet Cell Genet 21:177-83, 1978. Pubmed reference: 149653. DOI: 10.1159/000130895.

Equus kiang (kiang) :

2023

Zhou, C., Zheng, X., Peng, K., Feng, K., Yue, B., Wu, Y. :

Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation. Integr Zool 19:1199-1210, 2023. Pubmed reference: 38151756. DOI: 10.1111/1749-4877.12795.

2021

Zeng, L., Liu, H.Q., Tu, X.L., Ji, C.M., Gou, X., Esmailizadeh, A., Wang, S., Wang, M.S., Wang, M.C., Li, X.L., Charati, H., Adeola, A.C., Moshood Adedokun, R.A., Oladipo, O., Olaogun, S.C., Sanke, O.J., Godwin F, M., Cecily Ommeh, S., Agwanda, B., Kasiiti Lichoti, J., Han, J.L., Zheng, H.K., Wang, C.F., Zhang, Y.P., Frantz, L.A.F., Wu, D.D. :

Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 42:2095-8137(2021)04-0450-11:450-460, 2021. Pubmed reference: 34156172. DOI: 10.24272/j.issn.2095-8137.2021.095.

2011

Luo, Y., Chen, Y., Liu, F., Jiang, C., Gao, Y. :

Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang). Mitochondrial DNA 22:6-8, 2011. Pubmed reference: 21732718. DOI: 10.3109/19401736.2011.588221.

2009

Musilova, P., Kubickova, S., Horin, P., Vodicka, R., Rubes, J. :

Equus przewalskii (Przewalski's horse) :

2025

Faulk, C. :

Sequencing and assembling the genome of Przewalski's horse in the classroom. J Equine Vet Sci 147:105383, 2025. Pubmed reference: 39961497. DOI: 10.1016/j.jevs.2025.105383.

2024

Flack, N., Hughes, L., Cassens, J., Enriquez, M., Gebeyehu, S., Alshagawi, M., Hatfield, J., Kauffman, A., Brown, B., Klaeui, C., Mabrouk, I.F., Walls, C., Yeater, T., Rivas, A., Faulk, C. :

The genome of Przewalski's horse (Equus ferus przewalskii). bioRxiv , 2024. Pubmed reference: 38464182. DOI: 10.1101/2024.02.20.581252.

Flack, N., Hughes, L., Cassens, J., Enriquez, M., Gebeyehu, S., Alshagawi, M., Hatfield, J., Kauffman, A., Brown, B., Klaeui, C., Mabrouk, I.F., Walls, C., Yeater, T., Rivas, A., Faulk, C. :

The genome of Przewalski's horse (Equus ferus przewalskii). G3 (Bethesda) 14:jkae113, 2024. Pubmed reference: 38805182. DOI: 10.1093/g3journal/jkae113.

2023

Tang, X., Zhu, B., Ren, R., Chen, B., Li, S., Gu, J. :

1974

Short, R.V., Chandley, A.C., Jones, R.C., Allen, W.R. :

Meiosis in interspecific equine hybrids. II. The przewalski horse/domestic horse hybrid. Cytogenet Cell Genet 13:465-78, 1974. Pubmed reference: 4462982. DOI: 10.1159/000130300.

Equus quagga (plains zebra) :

2007

Musilova, P., Kubickova, S., Zrnova, E., Horin, P., Vahala, J., Rubes, J. :

2003

Yang, F., Fu, B., O'Brien, P.C., Robinson, T.J., Ryder, O.A., Ferguson-Smith, M.A. :

Karyotypic relationships of horses and zebras: results of cross-species chromosome painting. Cytogenet Genome Res 102:235-43, 2003. Pubmed reference: 14970709. DOI: 10.1159/000075755.

Equus zebra (mountain zebra) :

2002

Raudsepp, T., Lear, T.L., Chowdhary, B.P. :

Comparative mapping in equids: the asine X chromosome is rearranged compared to horse and Hartmann's mountain zebra. Cytogenet Genome Res 96:206-9, 2002. Pubmed reference: 12438800. DOI: 10.1159/000063050.

2001

Richard, F., Messaoudi, C., Lombard, M., Dutrillaux, B. :

Chromosome homologies between man and mountain zebra (Equus zebra hartmannae) and description of a new ancestral synteny involving sequences homologous to human chromosomes 4 and 8. Cytogenet Cell Genet 93:291-6, 2001. Pubmed reference: 11528128. DOI: 10.1159/000057000.

Eremias argus :

2023

Li, W., Du, J., Yang, L., Liang, Q., Yang, M., Zhou, X., Du, W. :

Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards. BMC Biol 21:40, 2023. Pubmed reference: 36803146. DOI: 10.1186/s12915-023-01535-z.

Eretmochelys imbricata (hawksbill sea turtle) :

2025

2023

Guo, Y., Tang, J., Zhuo, Z., Huang, J., Fu, Z., Song, J., Liu, M., Dong, Z., Wang, Z. :

The first high-quality chromosome-level genome of Eretmochelys imbricata using HiFi and Hi-C data. Sci Data 10:604, 2023. Pubmed reference: 37689728. DOI: 10.1038/s41597-023-02522-3.

Eryx miliaris (dwarf sand boa) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Esox lucius (northern pike) :

2024

Johnson, H.A., Rondeau, E.B., Sutherland, B.J.G., Minkley, D.R., Leong, J.S., Whitehead, J., Despins, C.A., Gowen, B.E., Collyard, B.J., Whipps, C.M., Farrell, J.M., Koop, B.F. :

Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing. G3 (Bethesda) 14:jkae183, 2024. Pubmed reference: 39115373. DOI: 10.1093/g3journal/jkae183.

Esox reichertii (Amur pike) :

2025

Zhang, Y., Zhang, Y., Huo, T., Qogt, G., Zhang, P., Zhang, H., Jia, Z. :

Chromosome-level genome assembly and annotation of Amur Pike (Esox reichertii). Sci Data 12:1454, 2025. Pubmed reference: 40835863. DOI: 10.1038/s41597-025-05819-7.

Etroplus suratensis :

2024

Katneni, V.K., Krishnan, K., Prabhudas, S.K., Jayaraman, R., Quraishi, N., Vasagam, K., Jangam, A.K., Angel, J.R.J., Kaikkolante, N., Jayaraman, K., Mudagandur, S.S. :

Genome assembly at chromosome scale with telomere ends for Pearlspot, Etroplus suratensis. Sci Data 11:1226, 2024. Pubmed reference: 39537670. DOI: 10.1038/s41597-024-04096-0.

Eublepharis macularius (Leopard gecko) :

2023

Pinto, B.J., Gamble, T., Smith, C.H., Keating, S.E., Havird, J.C., Chiari, Y. :

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly. J Hered 114:513-520, 2023. Pubmed reference: 36869788. DOI: 10.1093/jhered/esad016.

Eucyclogobius newberryi (tidewater goby) :

2024

Jacobs, D.K., Kinziger, A., Abrecht, M., McCraney, W.T., Hà, B.A., Spies, B.T., Heath-Heckman, E., Marimuhtu, M.P.A., Nguyen, O., Fairbairn, C.W., Seligmann, W.E., Escalona, M., Miller, C., Shaffer, H.B. :

Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi. J Hered 116:170-178, 2024. Pubmed reference: 39367793. DOI: 10.1093/jhered/esae053.

Eudorcas rufifrons (Red-fronted gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Eudorcas thomsonii (Thomson's gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Eulemur rufifrons (Bennett's brown lemur) :

2025

Hauff, L., Rasoanaivo, N.E., Razafindrakoto, A., Ravelonjanahary, H., Wright, P.C., Rakotoarivony, R., Bergey, C.M. :

De novo genome assembly for an endangered lemur using portable Nanopore sequencing in rural Madagascar. Ecol Evol 15:e70734, 2025. Pubmed reference: 39777412. DOI: 10.1002/ece3.70734.

Everson, K.M., Black, A.N., Donohue, M.E., Weisrock, D.W. :

An annotated chromosome-level genome for the red-fronted brown lemur (Eulemur rufifrons) sheds light on brown lemur evolution. G3 (Bethesda) 15:jkaf213, 2025. Pubmed reference: 40931566. DOI: 10.1093/g3journal/jkaf213.

Eumicrotremus spinosus (Atlantic spiny lumpsucker) :

2023

Pinninti, L.R., Maurstad, M.F., Hoff, S.N.K., Kristensen, T., Noble, L.R., Jentoft, S., Fernandes, J.M.O. :

The complete mitochondrial genome of the Atlantic spiny lumpsucker Eumicrotremus spinosus (Fabricius, 1776). Mitochondrial DNA B Resour 8:364-367, 2023. Pubmed reference: 36926640. DOI: 10.1080/23802359.2023.2184649.

Eupleurogrammus muticus (smallhead hairtail) :

2024

Han, F.Y., Wu, R.X., Miao, B.B., Niu, S.F., Wang, Q.H., Liang, Z.B. :

Whole-genome sequencing analyses reveal the whip-like tail formation, innate immune evolution, and DNA repair mechanisms of Eupleurogrammus muticus. Animals (Basel) 14:434, 2024. Pubmed reference: 38338077. DOI: 10.3390/ani14030434.

Euprepiophis perlaceus (Szechwan rat snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Falco rusticolus (gyrfalcon) :

2025

Al-Ajli, F.O., Formenti, G., Fedrigo, O., Tracey, A., Sims, Y., Howe, K., Al-Karkhi, I.M., Althani, A.A., Jarvis, E.D., Rahman, S., Ayub, Q. :

Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia. Sci Rep 15:4154, 2025. Pubmed reference: 39900672. DOI: 10.1038/s41598-025-88216-9.

Falconiformes :

2024

Catanach, T., Hains, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 30 species of falcons (Falconiformes, Aves). Biodivers Genomes 2024, 2024. Pubmed reference: 39741639. DOI: 10.56179/001c.127653.

Felis catus (domestic cat) :

2025

Harris, A.J., Raudsepp, T., Foley, N.M., Warren, W.C., Lyons, L.A., Murphy, W.J. :

Near-gapless genome assemblies of the domestic cat (Felis silvestris catus) and the African serval (Leptailurus serval) derived from trio-binning. J Hered 116:818-825, 2025. Pubmed reference: 40600648. DOI: 10.1093/jhered/esaf047.

2024

Matsumoto, Y., Yik-Lok Chung, C., Isobe, S., Sakamoto, M., Lin, X., Chan, T.F., Hirakawa, H., Ishihara, G., Lam, H.M., Nakayama, S., Sasamoto, S., Tanizawa, Y., Watanabe, A., Watanabe, K., Yagura, M., Niimura, Y., Nakamura, Y. :

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats. J Adv Res 75:863-874, 2024. Pubmed reference: 39490737. DOI: 10.1016/j.jare.2024.10.023.

2023

Duhan, N., Kaur, S., Kaundal, R. :

Patterson, E.C., Lall, G.M., Neumann, R., Ottolini, B., Sacchini, F., Foster, A.P., Jobling, M.A., Wetton, J.H. :

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 67:102944, 2023. Pubmed reference: 37820546. DOI: 10.1016/j.fsigen.2023.102944.

2022

Hernandez, I., Hayward, J.J., Brockman, J.A., White, M.E., Mouttham, L., Wilcox, E.A., Garrison, S., Castelhano, M.G., Loftus, J.P., Gomes, F.E., Balkman, C., Brooks, M.B., Fiani, N., Forman, M., Kern, T., Kornreich, B., Ledbetter, E.C., Peralta, S., Struble, A.M., Caligiuri, L., Corey, E., Lin, L., Jordan, J., Sack, D., Boyko, A.R., Lyons, L.A., Todhunter, R.J. :

Complex feline disease mapping using a dense genotyping array. Front Vet Sci 9:862414, 2022. Pubmed reference: 35782544. DOI: 10.3389/fvets.2022.862414.

2021

de Groot, M., Anderson, H., Bauer, H., Bauguil, C., Bellone, R.R., Brugidou, R., Buckley, R.M., Dovč, P., Forman, O., Grahn, R.A., Kock, L., Longeri, M., Mouysset-Geniez, S., Qiu, J., Sofronidis, G., van der Goor, L.H.P., Lyons, L.A. :

Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet 52:675-682, 2021. Pubmed reference: 34143521. DOI: 10.1111/age.13100.

2020

Zhang, W., Schoenebeck, J.J. :

The ninth life of the cat reference genome, Felis_catus. PLoS Genet 16:e1009045, 2020. Pubmed reference: 33091014. DOI: 10.1371/journal.pgen.1009045.

Buckley, R.M., Davis, B.W., Brashear, W.A., Farias, F.H.G., Kuroki, K., Graves, T., Hillier, L.W., Kremitzki, M., Li, G., Middleton, R.P., Minx, P., Tomlinson, C., Lyons, L.A., Murphy, W.J., Warren, W.C. :

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16:e1008926, 2020. Pubmed reference: 33090996. DOI: 10.1371/journal.pgen.1008926.

Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :

Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis). J Hered 112:165-73, 2020. Pubmed reference: 33305796. DOI: 10.1093/jhered/esaa057.

2019

Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Ginns, E.I., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, G.D., Warren, W.C., Wasim, M., Lyons, L.A. :

Author Correction: Applications and efficiencies of the first cat 63 K DNA array. Sci Rep 9:4664, 2019. Pubmed reference: 30858384. DOI: 10.1038/s41598-018-38073-6.

2018

Gandolfi, B., Alhaddad, H., Abdi, M., Bach, L.H., Creighton, E.K., Davis, B.W., Decker, J.E., Dodman, N.H., Grahn, J.C., Grahn, R.A., Haase, B., Haggstrom, J., Hamilton, M.J., Helps, C.R., Kurushima, J.D., Lohi, H., Longeri, M., Malik, R., Meurs, K.M., Montague, M.J., Mullikin, J.C., Murphy, W.J., Nilson, S.M., Pedersen, N.C., Peterson, C.B., Rusbridge, C., Saif, R., Shelton, D.G., Warren, W.C., Wasim, M., Lyons, L.A. :

Applications and efficiencies of the first cat 63K DNA array. Sci Rep 8:7024, 2018. Pubmed reference: 29728693. DOI: 10.1038/s41598-018-25438-0.

Author Correction: Applications and efficiencies of the first cat 63K DNA array. Sci Rep 8:8746, 2018. Pubmed reference: 29867197. DOI: 10.1038/s41598-018-26885-5.

2016

Li, G., Hillier, L.W., Grahn, R., Zimin, A.V., David, V.A., Menotti-Raymond, M., Middleton, R., Hannah, S., Hendrickson, S., Makunin, A., O'Brien, S.J., Minx, P., Wilson, R.K., Lyons, L.A., Warren, W.C., Murphy, W.J. :

A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda) 6:1607-16, 2016. Pubmed reference: 27172201. DOI: 10.1534/g3.116.028746.

2014

Willet, C.E., Haase, B. :

An updated felCat5 SNP manifest for the Illumina Feline 63k SNP genotyping array. Anim Genet 45:614-5, 2014. Pubmed reference: 24804964. DOI: 10.1111/age.12169.

Tamazian, G., Simonov, S., Dobrynin, P., Makunin, A., Logachev, A., Komissarov, A., Shevchenko, A., Brukhin, V., Cherkasov, N., Svitin, A., Koepfli, K.P., Pontius, J., Driscoll, C.A., Blackistone, K., Barr, C., Goldman, D., Antunes, A., Quilez, J., Lorente-Galdos, B., Alkan, C., Marques-Bonet, T., Menotti-Raymond, M., David, V.A., Narfström, K., O'Brien, S.J. :

Annotated features of domestic cat - Felis catus genome. Gigascience 3:13, 2014. Pubmed reference: 25143822. DOI: 10.1186/2047-217X-3-13.

Montague, M.J., Li, G., Gandolfi, B., Khan, R., Aken, B.L., Searle, S.M., Minx, P., Hillier, L.W., Koboldt, D.C., Davis, B.W., Driscoll, C.A., Barr, C.S., Blackistone, K., Quilez, J., Lorente-Galdos, B., Marques-Bonet, T., Alkan, C., Thomas, G.W., Hahn, M.W., Menotti-Raymond, M., O'Brien, S.J., Wilson, R.K., Lyons, L.A., Murphy, W.J., Warren, W.C. :

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A 111:17230-5, 2014. Pubmed reference: 25385592. DOI: 10.1073/pnas.1410083111.

2012

Bach, L.H., Gandolfi, B., Grahn, J.C., Millon, L.V., Kent, M.S., Narfstrom, K., Cole, S.A., Mullikin, J.C., Grahn, R.A., Lyons, L.A. :

A high-resolution 15,000(Rad) radiation hybrid panel for the domestic cat. Cytogenet Genome Res 137:7-14, 2012. Pubmed reference: 22777158. DOI: 10.1159/000339416.

2010

Mullikin, J.C., Hansen, N.F., Shen, L., Ebling, H., Donahue, W.F., Tao, W., Saranga, D.J., Brand, A., Rubenfield, M.J., Young, A.C., Cruz, P. :

Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics 11:406, 2010. Pubmed reference: 20576142. DOI: 10.1186/1471-2164-11-406.

2009

Menotti-Raymond, M., David, V.A., Schäffer, A.A., Tomlin, J.F., Eizirik, E., Phillip, C., Wells, D., Pontius, J.U., Hannah, S.S., O'Brien, S.J. :

An autosomal genetic linkage map of the domestic cat, Felis silvestris catus. Genomics 93:305-13, 2009. Pubmed reference: 19059333. DOI: 10.1016/j.ygeno.2008.11.004.

2008

Borodin, P.M., Karamysheva, T.V., Rubtsov, N.B. :

[Immunofluorescent analysis of meiotic recombination and interference in the domestic cat]. Tsitologiia 50:62-6, 2008. Pubmed reference: 18409370.

O'Brien, S.J., Johnson, W., Driscoll, C., Pontius, J., Pecon-Slattery, J., Menotti-Raymond, M. :

State of cat genomics. Trends Genet 24:268-79, 2008. Pubmed reference: 18471926. DOI: 10.1016/j.tig.2008.03.004.

2007

Pontius, J.U., Mullikin, J.C., Smith, D.R., Agencourt Sequencing Team et al. :

Initial sequence and comparative analysis of the cat genome. Genome Res 17:1675-89, 2007. Pubmed reference: 17975172. DOI: 10.1101/gr.6380007.

2006

Murphy, W.J. :

The feline genome. Genome Dyn 2:60-8, 2006. Pubmed reference: 18753769. DOI: 10.1159/000095093.

2003

Menotti-Raymond, M., David, V.A., Roelke, M.E., Chen, Z.Q., Menotti, K.A., Sun, S., Schäffer, A.A., Tomlin, J.F., Agarwala, R., O'Brien, S.J., Murphy, W.J. :

Second-generation integrated genetic linkage/radiation hybrid maps of the domestic cat (Felis catus). J Hered 94:95-106, 2003. Pubmed reference: 12692169. DOI: 10.1093/jhered/esg008.

2002

O'Brien, S.J., Menotti-Raymond, M., Murphy, W.J., Yuhki, N. :

The Feline Genome Project. Annu Rev Genet 36:657-86, 2002. Pubmed reference: 12359739. DOI: 10.1146/annurev.genet.36.060602.145553.

2001

Sun, S., Murphy, W.J., Menotti-Raymond, M., O'Brien, S.J. :

Integration of the feline radiation hybrid and linkage maps. Mamm Genome 12:436-41, 2001. Pubmed reference: 11353390. DOI: 10.1007/s003350010289.

2000

Murphy, W.J., Sun, S., Chen, Z.Q., Yuhki, N., Hirschmann, D., Menotti-Raymond, M., O'Brien, S.J. :

A radiation hybrid map of the cat genome: Implications for comparative mapping Genome Research 10:691-702, 2000. Pubmed reference: 10810092.

1999

Menotti-Raymond, M., David, V.A., Lyons, L.A., Schäffer, A.A., Tomlin, J.F., Hutton, M.K., O'Brien, S.J. :

A genetic linkage map of microsatellites in the domestic cat (Felis catus). Genomics 57:9-23, 1999. Pubmed reference: 10191079. DOI: 10.1006/geno.1999.5743.

1997

Obrien, S.J., Cevario, S.J., Martenson, J.S., Thompson, M.A., Nash, W.G., Chang, E., Graves, J.A.M., Spencer, J.A., Cho, K.W., Tsujimoto, H., Lyons, L.A. :

Comparative gene mapping in the domestic cat (felis catus) Journal of Heredity 88:408-414, 1997. Pubmed reference: 9378918.

Obrien, S.J., Wienberg, J., Lyons, L.A. :

Comparative genomics - lessons from cats [Review] Trends in Genetics 13:393-399, 1997. Pubmed reference: 9351340.

1996

Hirota, J., Usui, R., Satoh, T., Ikemoto, S. :

Telomere position on the cat chromosome. J Vet Med Sci 58:1025-6, 1996. Pubmed reference: 8916006. DOI: 10.1292/jvms.58.10_1025.

1995

Rettenberger, G., Klett, C., Zechner, U., Bruch, J., Just, W., Vogel, W., Hameister, H. :

ZOO-FISH analysis - cat and human karyotypes closely resemble the putative ancestral mammalian karyotype Chromosome Research 3:479-486, 1995. Pubmed reference: 8581300.

Yakimenko, L.V., Korablev, V.P., Yudin, V.G., Seredkina, M.A. :

Cytogenetic study of Felis euptilura and the hybrids F-catus x F-euptilura (Carnivora, Felidae). Zoologichesky Zhurnal 74:143-148, 1995.

1993

Stanyon, R., Bigoni, F., Wienberg, J., Hadidian, J. :

A Standardized G-Banded Karyotype for the Raccoon (Procyon lotor) Compared with the Domestic Cat. Bollettino di Zoologia 60:41-45, 1993.

1990

Kalat, M., Mayr, B., Schleger, W. :

Sequential Counterstain- Enhanced Banding - Heterochromatin Characterization in the Domestic Cat (Felis-Catus). Caryologia 43:183-189, 1990.

1987

Grafodatskiĭ, A.S., Biltueva, L.S. :

[Homology of G-banded mammalian chromosomes]. Genetika 23:93-103, 1987. Pubmed reference: 3469125.

Shibasaki, Y., Flou, S., Rønne, M. :

The R-banded karyotype of Felis catus. Cytobios 51:35-47, 1987. Pubmed reference: 3622005.

1982

O'Brien, S.J., Nash, W.G. :

Genetic mapping in mammals: chromosome map of domestic cat. Science 216:257-65, 1982. Pubmed reference: 7063884. DOI: 10.1126/science.7063884.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1963

Matano, J. :

A study of the chromosomes in the cat. Japanese Journal of Genetics 38:147-156, 1963.

Felis nigripes (black-footed cat) :

2024

Yuan, J., Kitchener, A.C., Lackey, L.B., Sun, T., Jiangzuo, Q., Tuohetahong, Y., Zhao, L., Yang, P., Wang, G., Huang, C., Wang, J., Hou, W., Liu, Y., Chen, W., Mi, D., Murphy, W.J., Li, G. :

The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 121:e2310763120, 2024. Pubmed reference: 38165928. DOI: 10.1073/pnas.2310763120.

Ficedula :

2014

Kawakami, T., Backström, N., Burri, R., Husby, A., Olason, P., Rice, A.M., Alund, M., Qvarnström, A., Ellegren, H. :

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array. Mol Ecol Resour 14:1248-60, 2014. Pubmed reference: 24784959. DOI: 10.1111/1755-0998.12270.

Fukomys anselli (Ansell's mole-rat) :

2025

Bekavac, M., Coimbra, R., Busa, V.F., Behm, M., Wagner, R.E., Goncalves, A., Begall, S., Frye, M., Odom, D.T. :

De novo genome assembly of Ansell's mole-rat (Fukomys anselli). G3 (Bethesda) :jkaf271, 2025. Pubmed reference: 41219156. DOI: 10.1093/g3journal/jkaf271.

Fulvetta ruficapilla :

2024

Yan, C., Si, S., Chen, H.M., Zhang, Y.T., Liu, L.M., Wu, F., Wang, M.S. :

A high-quality genome assembly of the Spectacled Fulvetta (Fulvetta ruficapilla) endemic to China. Sci Data 11:1252, 2024. Pubmed reference: 39567527. DOI: 10.1038/s41597-024-04094-2.

Furcifer pardalis :

2023

Xie, H., Chen, Z., Pang, S., Du, W. :

Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome. Genome Biol Evol 15:evad131, 2023. Pubmed reference: 37481259. DOI: 10.1093/gbe/evad131.

Gadus morhua (Atlantic cod) :

2024

Jentoft, S., Tørresen, O.K., Tooming-Klunderud, A., Skage, M., Kollias, S., Jakobsen, K.S. :

The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758). Wellcome Open Res 9:189, 2024. Pubmed reference: 39224768. DOI: 10.12688/wellcomeopenres.21122.1.

2012

Ghigliotti, L., Fevolden, S.E., Cheng, C.H., Babiak, I., Dettai, A., Pisano, E. :

Karyotyping and cytogenetic mapping of Atlantic cod (Gadus morhua Linnaeus, 1758). Anim Genet 43:746-52, 2012. Pubmed reference: 22497346. DOI: 10.1111/j.1365-2052.2012.02343.x.

2009

Higgins, B., Hubert, S., Simpson, G., Stone, C., Bowman, S. :

Characterization of 155 EST-derived microsatellites from Atlantic cod (Gadus morhua) and validation for linkage mapping. Mol Ecol Resour 9:733-7, 2009. Pubmed reference: 21564732. DOI: 10.1111/j.1755-0998.2008.02475.x.

Gallirallus australis (weka) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

Gallus gallus (chicken) :

2025

Ashari, H., Liu, L.S., Dagong, M.I.A., Cai, Z.F., Xie, G.L., Yin, T.T., Zhang, Y.P., Han, J.L., Peng, M.S. :

Genome sequencing and assembly of feral chickens in the wild of Sulawesi, Indonesia. Anim Genet 56:e13497, 2025. Pubmed reference: 39710860. DOI: 10.1111/age.13497.

Shin, H.D., Park, W., Chai, H.H., Lee, Y., Jung, J., Ko, B.J., Kim, H. :

Chromosome-level genome assembly of Korean long-tailed chicken and pangenome of 40 Gallus gallus assemblies. Sci Data 12:51, 2025. Pubmed reference: 39799174. DOI: 10.1038/s41597-024-04287-9.

Zhao, Q., Yin, Z., Hou, Z. :

Gou, Y., Jing, Y., Wang, Y., Li, X., Yang, J., Wang, K., He, H., Yang, Y., Tang, Y., Wang, C., Xu, J., Yang, F., Li, M., Tang, Q. :

Guan, D., Bai, Z., Zhu, X., Zhong, C., Hou, Y., Zhu, D. :

Genetic regulation of gene expression across multiple tissues in chickens. Nat Genet 57:1298-1308, 2025. Pubmed reference: 40200121. DOI: 10.1038/s41588-025-02155-9.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Zhu, D., Wang, Y., Qu, H., Feng, C., Zhang, H., Sheng, Z., Jiang, Y., Nie, Q., Chu, S., Shu, D., Jiang, Z., Zhang, D., Fang, L., Li, H., Xu, Z., Zhao, Y., Wang, Y., Hu, X. :

GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes. Genomics Proteomics Bioinformatics 23:qzaf032, 2025. Pubmed reference: 40234734. DOI: 10.1093/gpbjnl/qzaf032.

Wang, C., Lei, B., Bao, Y., Wang, Z., Chen, C., Zhang, Y., Qin, S., Sun, T., Tang, Z., Liu, Y. :

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes. iScience 28:112049, 2025. Pubmed reference: 40104067. DOI: 10.1016/j.isci.2025.112049.

de Lima, A.O., Ng, T.T., Sparling, B., Griggs, L.M., Lai, K., Drechsler, Y., Hawkins, R.D. :

An updated Gallus gallus genome annotation through multi-tissue transcriptome analysis. Genomics 117:111056, 2025. Pubmed reference: 40383208. DOI: 10.1016/j.ygeno.2025.111056.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Hou, Y., Zou, D., Chu, Q., Zhan, B., Wang, R., Guan, D., Wang, W., Feng, X., Li, X., Zhu, X., Bai, Z., Gao, Y., Yin, H., Xu, T., Yuan, Z., Hu, X., Yang, N., Zhou, H., Fang, L., Zhang, Z. :

The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity. Nucleic Acids Res :gkaf731, 2025. Pubmed reference: 40827640. DOI: 10.1093/nar/gkaf731.

2024

Tan, X., Zhang, J., Dong, J., Huang, M., Li, Q., Wang, H., Bai, L., Cui, M., Zhou, Z., Yang, S., Wang, D. :

Whole-genome variants dataset of 209 local chickens from China. Sci Data 11:169, 2024. Pubmed reference: 38316816. DOI: 10.1038/s41597-024-02995-w.

Wu, S., Wang, K., Dou, T., Yuan, S., Yan, S., Xu, Z., Liu, Y., Jian, Z., Zhao, J., Zhao, R., Zi, X., Gu, D., Liu, L., Li, Q., Wu, D.D., Jia, J., Su, Z., Ge, C. :

High quality assemblies of four indigenous chicken genomes and related functional data resources. Sci Data 11:300, 2024. Pubmed reference: 38490983. DOI: 10.1038/s41597-024-03126-1.

Zhao, X., Wen, J., Zhang, X., Zhang, J., Zhu, T., Wang, H., Yang, W., Cao, G., Xiong, W., Liu, Y., Qu, C., Ning, Z., Qu, L. :

Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 15:45, 2024. Pubmed reference: 38556896. DOI: 10.1186/s40104-024-01006-7.

Degalez, F., Charles, M., Foissac, S., Zhou, H., Guan, D., Fang, L., Klopp, C., Allain, C., Lagoutte, L., Lecerf, F., Acloque, H., Giuffra, E., Pitel, F., Lagarrigue, S. :

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 14:6588, 2024. Pubmed reference: 38504112. DOI: 10.1038/s41598-024-56705-y.

Wu, S., Wang, K., Dou, T., Yuan, S., Yan, S., Xu, Z., Liu, Y., Jian, Z., Zhao, J., Zhao, R., Zi, X., Gu, D., Liu, L., Li, Q., Wu, D.D., Jia, J., Su, Z., Ge, C. :

Author Correction: High quality assemblies of four indigenous chicken genomes and related functional data resources. Sci Data 11:354, 2024. Pubmed reference: 38589395. DOI: 10.1038/s41597-024-03203-5.

Wu, S., Dou, T., Yuan, S., Yan, S., Xu, Z., Liu, Y., Jian, Z., Zhao, J., Zhao, R., Zi, X., Gu, D., Liu, L., Li, Q., Wu, D.D., Jia, J., Ge, C., Su, Z., Wang, K. :

Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents. BMC Genomics 25:430, 2024. Pubmed reference: 38693501. DOI: 10.1186/s12864-024-10316-z.

Degalez, F., Bardou, P., Lagarrigue, S. :

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations. NAR Genom Bioinform 6:lqae101, 2024. Pubmed reference: 39157583. DOI: 10.1093/nargab/lqae101.

Qiu, H., Ning, T., Gong, W., Sun, H., Mu, G., Li, J. :

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl. Sci Data 11:1163, 2024. Pubmed reference: 39438465. DOI: 10.1038/s41597-024-04014-4.

Ren, J., Kou, W., Xu, Y., Lu, M., Gong, M., Wang, X., Zhang, X., Liu, Z., Li, H., Yang, Q., Shah, A.M., Zhu, F., Hou, Z.C., Xu, N., Jiang, Y., Wang, F. :

Pan-genome analyses add ∼1000 genes to the "complete" genome assembly of chicken. J Genet Genomics 52:116-119, 2024. Pubmed reference: 39510408. DOI: 10.1016/j.jgg.2024.10.009.

Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., Ladjali-Mohammedi, K. :

Rabbani, M.A.G., Vallejo-Trujillo, A., Wu, Z., Miedzinska, K., Faruque, S., Watson, K.A., Smith, J. :

Whole genome sequencing of three native chicken varieties (Common Deshi, Hilly and Naked Neck) of Bangladesh. Sci Data 11:1432, 2024. Pubmed reference: 39719437. DOI: 10.1038/s41597-024-04291-z.

2023

Huang, Z., Xu, Z., Bai, H., Huang, Y., Kang, N., Ding, X., Liu, J., Luo, H., Yang, C., Chen, W., Guo, Q., Xue, L., Zhang, X., Xu, L., Chen, M., Fu, H., Chen, Y., Yue, Z., Fukagawa, T., Liu, S., Chang, G., Xu, L. :

Evolutionary analysis of a complete chicken genome. Proc Natl Acad Sci U S A 120:e2216641120, 2023. Pubmed reference: 36780517. DOI: 10.1073/pnas.2216641120.

Jin, S., Jia, Y., Jiang, L., Cao, C., Ding, Y., Zhang, T., Liu, X., Li, Y., Geng, Z. :

Characteristics of the complete mitochondrial genome of Douhua chicken (Gallus gallus) and phylogenetic considerations. J Anim Sci 101:skad064, 2023. Pubmed reference: 36847733. DOI: 10.1093/jas/skad064.

Pan, Z., Wang, Y., Wang, M., Wang, Y., Zhu, X., Gu, S., Zhong, C., An, L., Shan, M., Damas, J., Halstead, M.M., Guan, D., Trakooljul, N., Wimmers, K., Bi, Y., Wu, S., Delany, M.E., Bai, X., Cheng, H.H., Sun, C., Yang, N., Hu, X., Lewin, H.A., Fang, L., Zhou, H. :

An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Sci Adv 9:eade1204, 2023. Pubmed reference: 37134160. DOI: 10.1126/sciadv.ade1204.

Xiong, X., Liu, J., Rao, Y. :

Whole Genome Resequencing Helps Study Important Traits in Chickens. Genes (Basel) 14:1198, 2023. Pubmed reference: 37372379. DOI: 10.3390/genes14061198.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Zhu, Q., Cai, Y., Xiao, C., Kong, L., Pan, X., Song, B., Song, Z. :

RNA sequencing transcriptomics and metabolomics in three poultry breeds. Sci Data 10:594, 2023. Pubmed reference: 37679362. DOI: 10.1038/s41597-023-02505-4.

Rice, E.S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J.R., Bardou, P., Blackmon, H., Charles, M., Cheng, H.H., Fedrigo, O., Fiddaman, S.R., Formenti, G., Frantz, L.A.F., Gilbert, M.T.P., Hearn, C.J., Jarvis, E.D., Klopp, C., Marcos, S., Mason, A.S., Velez-Irizarry, D., Xu, L., Warren, W.C. :

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 21:267, 2023. Pubmed reference: 37993882. DOI: 10.1186/s12915-023-01758-0.

Zhu, F., Yin, Z.T., Zhao, Q.S., Sun, Y.X., Jie, Y.C., Smith, J., Yang, Y.Z., Burt, D.W., Hincke, M., Zhang, Z.D., Yuan, M.D., Kaufman, J., Sun, C.J., Li, J.Y., Shao, L.W., Yang, N., Hou, Z.C. :

A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 6:1233, 2023. Pubmed reference: 38057566. DOI: 10.1038/s42003-023-05619-y.

2022

Smith, J., Alfieri, J.M., Anthony, N., Arensburger, P., Athrey, G.N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P.M., Carroll, R., Casono, M.C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L.M., Crooijmans, R., Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J.M., Derks, M., Diack, A.B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S.R., Formenti, G., Frantz, L.A.F., Fulton, J.E., Gaginskaya, E., Galkina, S., Gallardo, R.A., Geibel, J., Gheyas, A.A., Godinez, C.J.P., Goodell, A., Graves, J.A.M., Griffin, D.K., Haase, B., Han, J.L., Hanotte, O., Henderson, L.J., Hou, Z.C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E.D., Johnson, S.M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J.H., Klopp, C., Lagarrigue, S., Lamont, S.J., Lange, M., Lanke, A., Larkin, D.M., Larson, G., Layos, J.K.N., Lebrasseur, O., Malinovskaya, L.P., Martin, R.J., Martin Cerezo, M.L., Mason, A.S., McCarthy, F.M., McGrew, M.J., Mountcastle, J., Muhonja, C.K., Muir, W., Muret, K., Murphy, T.D., Ng'ang'a, I., Nishibori, M., O'Connor, R.E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H.R., Perini, F., Pigozzi, M.I., Potter, K.C., Price, P.D., Reimer, C., Rice, E.S., Rocos, N., Rogers, T.F., Saelao, P., Schauer, J., Schnabel, R.D., Schneider, V.A., Simianer, H., Smith, A., Stevens, M.P., Stiers, K., Tiambo, C.K., Tixier-Boichard, M., Torgasheva, A.A., Tracey, A., Tregaskes, C.A., Vervelde, L., Wang, Y., Warren, W.C., Waters, P.D., Webb, D., Weigend, S., Wolc, A., Wright, A.E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.T., Young, M.C., Zhang, G., Zhao, B., Zhou, H. :

Fourth report on chicken genes and chromosomes 2022. Cytogenet Genome Res 162:405-528, 2022. Pubmed reference: 36716736. DOI: 10.1159/000529376.

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

2019

Liu, R., Xing, S., Wang, J., Zheng, M., Cui, H., Crooijmans, R.P.M.A., Li, Q., Zhao, G., Wen, J. :

A new chicken 55K SNP genotyping array. BMC Genomics 20:410, 2019. Pubmed reference: 31117951. DOI: 10.1186/s12864-019-5736-8.

2018

Piégu, B., Arensburger, P., Guillou, F., Bigot, Y. :

But where did the centromeres go in the chicken genome models? Chromosome Res 26:297-306, 2018. Pubmed reference: 30225548. DOI: 10.1007/s10577-018-9585-0.

2014

Griffin, D., Burt, D.W. :

All chromosomes great and small: 10 years on. Chromosome Res 22:1-6, 2014. Pubmed reference: 24700106. DOI: 10.1007/s10577-014-9413-0.

2013

Kranis, A., Gheyas, A.A., Boschiero, C., Turner, F., Yu, L., Smith, S., Talbot, R., Pirani, A., Brew, F., Kaiser, P., Hocking, P.M., Fife, M., Salmon, N., Fulton, J., Strom, T.M., Haberer, G., Weigend, S., Preisinger, R., Gholami, M., Qanbari, S., Simianer, H., Watson, K.A., Woolliams, J.A., Burt, D.W. :

Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59, 2013. Pubmed reference: 23356797. DOI: 10.1186/1471-2164-14-59.

Gheyas, A.A., Burt, D.W. :

Microarray resources for genetic and genomic studies in chicken: A review. Genesis 51:337-56, 2013. Pubmed reference: 23468091. DOI: 10.1002/dvg.22387.

2011

Groenen, M.A., Megens, H.J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P., Vereijken, A., Okimoto, R., Muir, W.M., Cheng, H.H. :

The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274, 2011. Pubmed reference: 21627800. DOI: 10.1186/1471-2164-12-274.

2008

Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A.M., Crooijmans, R.P.M.A., Megens, H.-J., Zhang, H.M., McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P., Vereijken, A., Jungerius-Rattink, A., Albers, G.A.A., Taylor Lawley, C., Delaney, M.E., Cheng, H.H. :

Review of the initial validation and characterization of a chicken 3K SNP array. Worlds Poultry Science Journal 64:219-226, 2008.

2007

Burt, D.W., White, S.J. :

Avian genomics in the 21st century. Cytogenet Genome Res 117:6-13, 2007. Pubmed reference: 17675839. DOI: 10.1159/000103159.

2006

Burt, D.W. :

The chicken genome. Genome Dyn 2:123-37, 2006. Pubmed reference: 18753775. DOI: 10.1159/000095100.

Mu, Y.S., Li, H. :

[Latest progress on the chicken genome project]. Yi Chuan 28:617-22, 2006. Pubmed reference: 16735245.

2005

Burt, D.W. :

Chicken genome: current status and future opportunities. Genome Res 15:1692-8, 2005. Pubmed reference: 16339367. DOI: 10.1101/gr.4141805.

Schmid, M., Nanda, I., Hoehn, H., Schartl, M., Haaf, T., Buerstedde, J.M., Arakawa, H., Caldwell, R.B., Weigend, S., Burt, D.W., Smith, J., Griffin, D.K., Masabanda, J.S., Groenen, M.A., Crooijmans, R.P., Vignal, A., Fillon, V., Morisson, M., Pitel, F., Vignoles, M., Garrigues, A., Gellin, J., Rodionov, A.V., Galkina, S.A., Lukina, N.A., Ben-Ari, G., Blum, S., Hillel, J., Twito, T., Lavi, U., David, L., Feldman, M.W., Delany, M.E., Conley, C.A., Fowler, V.M., Hedges, S.B., Godbout, R., Katyal, S., Smith, C., Hudson, Q., Sinclair, A., Mizuno, S. :

Second report on chicken genes and chromosomes 2005. Cytogenet Genome Res 109:415-79, 2005. Pubmed reference: 15905640. DOI: 10.1159/000084205.

2004

Wong, G.K., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W., Li, G., Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, L.W., Yang, S.P., Warren, W.C., Wilson, R.K., Brandström, M., Ellegren, H., Crooijmans, R.P., van der Poel, J.J., Bovenhuis, H., Groenen, M.A., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J.R., Rogers, S., Walker, B.A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S.J., Zhou, H., Hocking, P.M., Morrice, D., de Koning, D.J., Law, A., Bartley, N., Burt, D.W., Hunt, H., Cheng, H.H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M.T., Andersson, B., Webber, C., Ponting, C.P., Overton, I.M., Boardman, P.E., Tang, H., Hubbard, S.J., Wilson, S.A., Yu, J., Wang, J., Yang, H. :

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-22, 2004. Pubmed reference: 15592405. DOI: 10.1038/nature03156.

Burt, D.W. :

Chicken genomics charts a path to the genome sequence. Brief Funct Genomic Proteomic 3:60-7, 2004. Pubmed reference: 15163360. DOI: 10.1093/bfgp/3.1.60.

International Chicken Genome Sequencing Consortium :

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716, 2004. Pubmed reference: 15592404. DOI: 10.1038/nature03154.

Wallis, J.W., Aerts, J., Groenen, M.A., Crooijmans, R.P., Layman, D., Graves, T.A., Scheer, D.E., Kremitzki, C., Fedele, M.J., Mudd, N.K., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S.P., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M.N., Cheng, H., de Jong, P.J., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J.D., Krzywinski, M., Schein, J., Hillier, L., Mardis, E.R., Wilson, R.K., Warren, W.C. :

A physical map of the chicken genome. Nature 432:761-4, 2004. Pubmed reference: 15592415. DOI: 10.1038/nature03030.

2003

Dodgson, J.B. :

Chicken genome sequence: a centennial gift to poultry genetics. Cytogenet Genome Res 102:291-6, 2003. Pubmed reference: 14970719. DOI: 75765.

2002

Smith, J., Paton, I.R., Murray, F., Crooijmans, R.P.M.A., Groenen, M.A.M., Burt, D.W. :

Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution Mammalian Genome 13:310-315, 2002. Pubmed reference: 12115034. DOI: 10.1007/s00335-001-3071-1.

2000

Smith, J., Paton, I.R., Bruley, C.K., Windsor, D., Burke, D., de, Leon, F.A.P., Burt, D.W. :

Integration of the genetic and physical maps of the chicken macrochromosomes Animal Genetics 31:20-27, 2000. Pubmed reference: 10690357.

Groenen, M.A.M., Cheng, H.H., Bumstead, N., Benkel, B.F., Briles, W.E., Burke, T., Burt, D.W., Crittenden, L.B., Dodgson, J., Hillel, J., Lamont, S., de, Leon, A.P., Soller, M., Takahashi, H., Vignal, A. :

A consensus linkage map of the chicken genome Genome Research 10:137-147, 2000. Pubmed reference: 10645958.

1998

Groenen, M.A.M., Crooijmans, R.P.M.A., Veenendaal, A., Cheng, H.H., Siwek, M., Vanderpoel, J.J. :

A comprehensive microsatellite linkage map of the chicken genome Genomics 49:265-274, 1998. Pubmed reference: 9598314. DOI: 10.1006/geno.1998.5225.

Burt, D.W., Cheng, H.H. :

The Chicken Gene Map. ILAR J 39:229-236, 1998. Pubmed reference: 11528082. DOI: 10.1093/ilar.39.2-3.229.

1997

Koi, M., Lamb, P.W., Filatov, L., Feinberg, A.P., Barrett, J.C. :

Construction of chicken x human microcell hybrids for human gene targeting Cytogenetics & Cell Genetics 76:72-76, 1997.

1996

Crooijmans, R.P.M.A., Vanoers, P.A.M., Strijk, J.A., Vanderpoel, J.J., Groenen, M.A.M. :

Preliminary linkage map of the chicken (gallus domesticus) genome based on microsatellite markers - 77 new markers mapped Poultry Science 75:746-754, 1996. Pubmed reference: 8737840.

Crittenden, L.B., Bitgood, J.J., Burt, D.W., Deleon, F.A.P., Tixierboichard, M. :

Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases Genetics Selection Evolution 28:289-297, 1996.

1995

Burt, D.W., Bumstead, N., Bitgood, J.J., Deleon, F.A.P., Crittenden, L.B. :

Chicken genome mapping: A new era in avian genetics Trends Genet 11:190-4, 1995. Pubmed reference: 7785078. DOI: 10.1016/s0168-9525(00)89042-3.

Cheng, H.H., Levin, I., Vallejo, R.L., Khatib, H., Dodgson, J.B., Crittenden, L.B., Hillel, J. :

Development of a genetic map of the chicken with markers of high utility Poultry Science 74:1855-1874, 1995. Pubmed reference: 8614694.

Ladjali, K., Bordas, A., Cribiu, E.P., Tixierboichard, M. :

Cytogenetic study of 2 lines of laying hens selected on residual food consumption [French]. Genetics Selection Evolution 27:313-322, 1995.

Ladjali, K., Tixier-Boichard, M., Cribiu, E.P. :

High- resolution chromosome preparations for G- and R-banding in Gallus domesticus. Journal of Heredity 86:136-139, 1995.

1994

Levin, I., Santangelo, L., Cheng, H., Crittenden, L.B., Dodgson, J.B. :

An Autosomal Genetic Linkage Map of the Chicken Journal of Heredity 85:79-85, 1994. Pubmed reference: 7910177.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1992

Bumstead, N., Palyga, J. :

A Preliminary Linkage Map of the Chicken Genome Genomics 13:690-697, 1992. Pubmed reference: 1353476.

Ponce de Leon, F.A., Li, Y., Weng, Z. :

Early and late replicative chromosomal banding patterns of Gallus domesticus. J Hered 83:36-42, 1992. Pubmed reference: 1372628. DOI: 10.1093/oxfordjournals.jhered.a111154.

1990

Bitgood, J.J., Somes, R.G. Jr :

Linkage relationships and gene mapping. In "Poultry Breeding and Genetics" (ed. R.D. Crawford), Elsevier, Amsterdam; Chapter 21 :469-495, 1990.

1989

Schmid, M., Enderle, E., Schindler, D., Schempp, W. :

Chromosome banding and DNA replication patterns in bird karyotypes. Cytogenet Cell Genet 52:139-46, 1989. Pubmed reference: 2630186. DOI: 10.1159/000132864.

1988

Okamoto, S., Maeda, Y., Hashiguchi, T. :

Analysis of the karyotypes of four species of jungle fowls. Japanese Journal of Zootechnical Science 59:146-151, 1988.

1987

Sohn, S.H., Ohh, B.K. :

[The chromosome number and morphology of Gallus domesticus] Korean Journal of Animal Sciences 29:535-542, 1987.

Auer, H., Mayr, B., Lambrou, M., Schleger, W. :

An extended chicken karyotype, including the NOR chromosome. Cytogenet Cell Genet 45:218-21, 1987. Pubmed reference: 3691189. DOI: 10.1159/000132457.

Sohn, S.H., Ohh, B.K. :

[Studies on the chromosomal marker by the G-banding patterns of chicken (Gallus domesticus)]. Korean Journal of Animal Sciences 29:543-548, 1987.

1986

Ansari, H.A., Takagi, N., Sasaki, M. :

Interordinal conservatism of chromosome banding patterns in Gallus domesticus (Galliformes) and Melopsittacus undulatus (Psittaciformes). Cytogenet Cell Genet 43:6-9, 1986. Pubmed reference: 3780317. DOI: 10.1159/000132290.

1981

Shoffner, R.N. :

Marker chromosomes and G-banding for location of genes in the chicken. Poult Sci 60:1372-5, 1981. Pubmed reference: 6948289. DOI: 10.3382/ps.0601372.

1957

Newcomer, E.H. :

The mitotic chromosomes of the domestic fowl. Journal of Heredity 48:227-234, 1957.

1949

Warren, DC. :

Linkage relations of autosomal factors in the fowl. Genetics 34:333-50, 1949. Pubmed reference: 17247319. DOI: 10.1093/genetics/34.3.333.

1933

Hutt, F.B. :

Genetics of the fowl. II. a four-gene autosomal linkage group. Genetics 18:82-94, 1933. Pubmed reference: 17246679. DOI: 10.1093/genetics/18.1.82.

Warren, D.C. :

Nine independently inherited autosomal factors in the domestic fowl. Genetics 18:68-81, 1933. Pubmed reference: 17246678. DOI: 10.1093/genetics/18.1.68.

1928

Serebrovsky, A.S., Petrov, S.G. :

A case of close autosomal linkage in the fowl Journal of Heredity 19:305-306, 1928.

1921

Haldane, J.B.S. :

Linkage in poultry. Science 54:663 only, 1921. Pubmed reference: 17816160. DOI: 10.1126/science.54.1409.663.

Gallus lafayetii (Ceylon junglefowl) :

1988

Okamoto, S., Maeda, Y., Hashiguchi, T. :

Analysis of the karyotypes of four species of jungle fowls. Japanese Journal of Zootechnical Science 59:146-151, 1988.

Gallus sonneratii (gray junglefowl) :

1988

Okamoto, S., Maeda, Y., Hashiguchi, T. :

Analysis of the karyotypes of four species of jungle fowls. Japanese Journal of Zootechnical Science 59:146-151, 1988.

Gallus varius (green junglefowl) :

1988

Okamoto, S., Maeda, Y., Hashiguchi, T. :

Analysis of the karyotypes of four species of jungle fowls. Japanese Journal of Zootechnical Science 59:146-151, 1988.

Gambelia wislizenii (longnose leopard lizard) :

2025

McGuire, J.A., Richmond, J.Q., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Cooper, R.D., Westphal, M., Fisher, R.N., Wang, I.J., Shaffer, H.B. :

Genome Resources-A chromosome-Level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, the first reference genome for the lizard family crotaphytidae. J Hered :esaf053, 2025. Pubmed reference: 40741976. DOI: 10.1093/jhered/esaf053.

Garra rufa :

2025

Kon, T., Kon-Nanjo, K., Handayani, K.S., Zang, L., Fahrurrozi, F., Simakov, O., Gultom, V.D.N., Shimada, Y. :

Chromosome-level genome assembly of the doctor fish (Garra rufa). Sci Data 12:765, 2025. Pubmed reference: 40346083. DOI: 10.1038/s41597-025-05101-w.

Gasterosteus aculeatus (three-spined stickleback) :

2025

Au, E.H., Weaver, S., Katikaneni, A., Wucherpfennig, J.I., Luo, Y., Mangan, R.J., Wund, M.A., Bell, M.A., Lowe, C.B. :

Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet. bioRxiv , 2025. Pubmed reference: 39975098. DOI: 10.1101/2025.02.06.636934.

Au, E.H., Weaver, S., Katikaneni, A., Wucherpfennig, J.I., Luo, Y., Mangan, R.J., Wund, M.A., Bell, M.A., Lowe, C.B. :

Genome sequence of a marine threespine stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet. G3 (Bethesda) 15:jkaf114, 2025. Pubmed reference: 40408318. DOI: 10.1093/g3journal/jkaf114.

Gavialis gangeticus (Gharial) :

2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346:1254449, 2014. Pubmed reference: 25504731. DOI: 10.1126/science.1254449.

Gazella cuvieri (Cuvier's gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Gazella dorcas (Dorcas gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Gazella erlangeri (Neumann's gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Gazella leptoceros (Rhim gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Gazella subgutturosa (goitered gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Giraffa camelopardalis (Northern giraffe) :

1996

Vermeesch, J.R., De Meurichy, W., Van Den Berghe, H., Marynen, P., Petit, P. :

Differences in the distribution and nature of the interstitial telomeric (TTAGGG)n sequences in the chromosomes of the Giraffidae, okapai (Okapia johnstoni), and giraffe (Giraffa camelopardalis): evidence for ancestral telomeres at the okapi polymorphic rob(5;26) fusion site. Cytogenet Cell Genet 72:310-5, 1996. Pubmed reference: 8641137. DOI: 10.1159/000134211.

Giraffa tippelskirchi (Maasai giraffe) :

2025

Kim, J., Rosen, B.D., Fumagalli, S.E., Kuhn, K.L., Long, A., Schoenebeck, J.J., Wu-Cavener, L., Zimin, A.V., Cavener, D.R., Smith, T.P.L., Phillippy, A.M., Koren, S., Rhie, A. :

Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet. bioRxiv , 2025. Pubmed reference: 41256564. DOI: 10.1101/2025.10.01.679366.

2019

Farré, M., Li, Q., Darolti, I., Zhou, Y., Damas, J., Proskuryakova, A.A., Kulemzina, A.I., Chemnick, L.G., Kim, J., Ryder, O.A., Ma, J., Graphodatsky, A.S., Zhang, G., Larkin, D.M., Lewin, H.A. :

An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience 8:giz090, 2019. Pubmed reference: 31367745. DOI: 10.1093/gigascience/giz090.

Glaucidium cuculoides :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Globicephala macrorhynchus (short-finned pilot whale) :

2023

Kang, H., Liu, Q., Seim, I., Zhang, W., Li, H., Gao, H., Lin, W., Lin, M., Zhang, P., Zhang, Y., Gao, H., Wang, Y., Qin, Y., Liu, M., Dong, L., Yang, Z., Zhang, Y., Han, L., Fan, G., Li, S. :

A genome and single-nucleus cerebral cortex transcriptome atlas of the short-finned pilot whale Globicephala macrorhynchus. Mol Ecol Resour 23:1108-1123, 2023. Pubmed reference: 36826393. DOI: 10.1111/1755-0998.13775.

Globicephala melas (long-finned pilot whale) :

1988

Andersen, L.W., Friedrich, U. :

The karyotype of the long-finned pilot whale, Globicephala melaena. Hereditas 109:245-51, 1988. Pubmed reference: 3230026. DOI: 10.1111/j.1601-5223.1988.tb00361.x.

Gloydius shedaoensis (Shedao Island pitviper) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Gnathanodon speciosus (golden trevally) :

2025

Fan, B., Guo, J., Lei, C., Yang, S., Meng, Z., Peng, J., Yang, Y., Shen, Y., Li, Y., Wang, L. :

Haplotype-resolved genomics identifies cyp19a1a as a candidate master sex-determining gene in golden trevally (Gnathanodon speciosus). iScience 28:113493, 2025. Pubmed reference: 41019367. DOI: 10.1016/j.isci.2025.113493.

Gobionotothen gibberifrons (humped rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Gopherus evgoodei (Goodes thornscrub tortoise) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Gorilla :

2025

Han, S., Riyahi, S., Huang, X., Kuhlwilm, M. :

A curated dataset of great ape genome diversity. Sci Data 12:1835, 2025. Pubmed reference: 41261097. DOI: 10.1038/s41597-025-06124-z.

Gorilla beringei beringei (eastern mountain gorilla) :

2025

Nelson, D.R., Muvunyi, R., Hazzouri, K.M., Tumushime, J.C., Nzayisenga, G., Julius, N., Meert, W., Karim, L., Coppieters, W., Munson, K.M., Yoo, D., Eichler, E.E., Salehi-Ashtiani, K., Twizere, J.C. :

A near telomere-to-telomere phased reference assembly for the male mountain gorilla. Sci Data 12:842, 2025. Pubmed reference: 40404646. DOI: 10.1038/s41597-025-05114-5.

Gorilla gorilla (western gorilla) :

2025

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Gorsachius magnificus :

2024

Zheng, C., Chen, Q., Huang, S., Song, W., Chen, G., Lin, H., Xu, C., Qian, X., Cheng, Y., Jiang, A., Fan, Z., Liu, Y. :

Chromosome-scale genome assembly of the critically endangered white-eared night-heron (Gorsachius magnificus). Sci Data 11:73, 2024. Pubmed reference: 38228677. DOI: 10.1038/s41597-023-02894-6.

Gouania willdenowi (blunt-snouted clingfish) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Gymnodraco acuticeps :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Gymnogyps californianus (California condor) :

2022

Romanov, M.N., Da, Y., Chemnick, L.G., Thomas, S.M., Dandekar, S.S., Papp, J.C., Ryder, O.A. :

Towards a Genetic Linkage Map of the California Condor, an Endangered New World Vulture Species. Animals (Basel) 12:3266, 2022. Pubmed reference: 36496789. DOI: 10.3390/ani12233266.

Gymnothorax reevesii (Reeve's moray) :

2023

Zhang, K., Huang, Y., Zhang, Y., Liang, R., Li, Q., Li, R., Zhao, X., Bian, C., Chen, Y., Wu, J., Shi, Q., Lin, L. :

A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Sci Data 10:501, 2023. Pubmed reference: 37516767. DOI: 10.1038/s41597-023-02394-7.

Gyps fulvus (Eurasian griffon) :

1989

Schmid, M., Enderle, E., Schindler, D., Schempp, W. :

Chromosome banding and DNA replication patterns in bird karyotypes. Cytogenet Cell Genet 52:139-46, 1989. Pubmed reference: 2630186. DOI: 10.1159/000132864.

Harpagifer antarcticus (Antarctic spiny plunderfish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Harpia harpyja (Harpy eagle) :

2024

Canesin, L.E.C., Vilaça, S.T., Oliveira, R.R.M., Al-Ajli, F., Tracey, A., Sims, Y., Formenti, G., Fedrigo, O., Banhos, A., Sanaiotti, T.M., Farias, I.P., Jarvis, E.D., Oliveira, G., Hrbek, T., Solferini, V., Aleixo, A. :

A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes. Sci Rep 14:19925, 2024. Pubmed reference: 39261501. DOI: 10.1038/s41598-024-70305-w.

Heloderma suspectum (Gila monster) :

2024

Webster, T.H., Vannan, A., Pinto, B.J., Denbrock, G., Morales, M., Dolby, G.A., Fiddes, I.T., DeNardo, D.F., Wilson, M.A. :

Lack of dosage balance and incomplete dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly. Genome Biol Evol 16:evae018, 2024. Pubmed reference: 38319079. DOI: 10.1093/gbe/evae018.

2023

Webster, T.H., Vannan, A., Pinto, B.J., Denbrock, G., Morales, M., Dolby, G.A., Fiddes, I.T., DeNardo, D.F., Wilson, M.A. :

Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly. bioRxiv , 2023. Pubmed reference: 37163099. DOI: 10.1101/2023.04.26.538436.

Hemiscyllium ocellatum (epaulette shark) :

2023

Sendell-Price, A.T., Tulenko, F.J., Pettersson, M., Kang, D., Montandon, M., Winkler, S., Kulb, K., Naylor, G.P., Phillippy, A., Fedrigo, O., Mountcastle, J., Balacco, J.R., Dutra, A., Dale, R.E., Haase, B., Jarvis, E.D., Myers, G., Burgess, S.M., Currie, P.D., Andersson, L., Schartl, M. :

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nat Commun 14:6628, 2023. Pubmed reference: 37857613. DOI: 10.1038/s41467-023-42238-x.

Hepsetus odoe (African pike characin) :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Herpailurus yagouaroundi (jaguarundi) :

2021

Tamazian, G., Dobrynin, P., Zhuk, A., Zhernakova, D.V., Perelman, P.L., Serdyukova, N.A., Graphodatsky, A.S., Komissarov, A., Kliver, S., Cherkasov, N., Scott, A.F., Mohr, D.W., Koepfli, K.P., O'Brien, S.J., Krasheninnikova, K. :

Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi. J Hered 112:540-548, 2021. Pubmed reference: 34146095. DOI: 10.1093/jhered/esab036.

Heterocephalus glaber (naked mole-rat) :

2024

Sokolowski, D.J., Miclăuş, M., Nater, A., Faykoo-Martinez, M., Hoekzema, K., Zuzarte, P., Monis, S., Alvi, S.A., Erdmann, J., Erdmann, A.L., Kumaragurubaran, R., Bayerl, J., Yoo, D., Karimpour, N., Ungerleider, K., Hou, H., Fergal, M., Hourlier, T., Clarke, Z.A., Lischer, H.E., Leordean, D.V., Jiang, Y., Pugh, T.J., Smith, E.S.J., Haggerty, L., Laird, D.J., Lilue, J., Holmes, M.M., Eichler, E.E., Bruggmann, R., Simpson, J.T., Balmus, G., Wilson, M.D. :

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology. bioRxiv , 2024. Pubmed reference: 39651266. DOI: 10.1101/2024.11.26.625329.

2023

Romanenko, S.A., Kliver, S.F., Serdyukova, N.A., Perelman, P.L., Trifonov, V.A., Seluanov, A., Gorbunova, V., Azpurua, J., Pereira, J.C., Ferguson-Smith, M.A., Graphodatsky, A.S. :

Hexagrammos otakii (fat greenling) :

2025

Li, L., Hu, F., Liu, D., Wang, X., Diao, J., Zhu, Y., Gao, F., Fan, Y., Jian, Y., Wang, X., Pan, L., Guo, W. :

A Chromosomal-level genome assembly and annotation of fat greenling (Hexagrammos otakii). Sci Data 12:78, 2025. Pubmed reference: 39814736. DOI: 10.1038/s41597-025-04368-3.

Hippoglossus hippoglossus (Atlantic halibut) :

2025

Sinani, V.K., Wilson, R.C., Nome, T., Acharya, U., Kommisrud, E., Wetten, M., Kent, M.P. :

Development and validation of a 70K SNP genotyping array for Atlantic halibut (Hippoglossus hippoglossus). BMC Genomics 26:924, 2025. Pubmed reference: 41102675. DOI: 10.1186/s12864-025-12128-1.

2023

Weise, E.M., Van Wyngaarden, M., Den Heyer, C., Mills Flemming, J., Kess, T., Einfeldt, A.L., Fisher, J.A.D., Ditta, R., Pare, G., Ruzzante, D.E. :

SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus). Mar Biotechnol (NY) 25:580-587, 2023. Pubmed reference: 37351707. DOI: 10.1007/s10126-023-10227-2.

Hippotragus equinus (roan antelope) :

1995

Robinson, T.J., Harley, E.H. :

Absence of geographic chromosomal variation in the roan and sable antelope and the cytogenetics of a naturally occurring hybrid. Cytogenet Cell Genet 71:363-9, 1995. Pubmed reference: 8521725. DOI: 10.1159/000134140.

Hippotragus niger (sable antelope) :

1995

Robinson, T.J., Harley, E.H. :

Histiodraco velifer :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Holacanthus passer (king angelfish) :

2024

Gatins, R., Arias, C.F., Sánchez, C., Bernardi, G., De León, L.F. :

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific. GigaByte 2024:gigabyte115, 2024. Pubmed reference: 38550358. DOI: 10.46471/gigabyte.115.

Hucho bleekeri (Sichuan taimen) :

2025

Zhang, X., Xiong, D., Jian, S., Jiang, Y., Wang, L. :

Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage. BMC Genomics 26:839, 2025. Pubmed reference: 41013207. DOI: 10.1186/s12864-025-12057-z.

Hyaena hyaena (striped hyena) :

1995

Langhe, R.S., Rane, U.B. :

Cytogenetic analysis of striped hyena (hyaena hyaena). Indian Veterinary Journal 72:835-837, 1995.

Hydrophis curtus (Shaw's sea snake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hydrophis major (olive-headed seasnake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hydrophis ornatus (reef sea snake) :

2023

Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L. :

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 21:284, 2023. Pubmed reference: 38066641. DOI: 10.1186/s12915-023-01772-2.

Hydropotes inermis (Chinese water deer) :

1997

Yang, F., O'Brien, P.C., Wienberg, J., Neitzel, H., Lin, C.C., Ferguson-Smith, M.A. :

Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi). Chromosoma 106:37-43, 1997. Pubmed reference: 9169585. DOI: 10.1007/s004120050222.

Hydrurga leptonyx (leopard seal) :

2025

Nebenführ, M., Hamadou, A.B., Aguilar, A., Borrell, A., Gkafas, G.A., Janke, A. :

Mediterranean monk seal (Monachus monachus) and leopard seal (Hydrurga leptonyx) de novo genomes to study the demographic history and genetic diversity of southern seals. BMC Biol 23:102, 2025. Pubmed reference: 40241156. DOI: 10.1186/s12915-025-02207-w.

Canitz, J., Kienle, S.S., van der Linde, K., Borras-Chavez, R., Sperou, E.S., Leahy, A., Rivera, S., Autenrieth, M., Hoffman, J.I., Bonin, C.A. :

Reference genome of the leopard seal (Hydrurga leptonyx), a Southern Ocean apex predator. Front Genet 16:1561273, 2025. Pubmed reference: 40438324. DOI: 10.3389/fgene.2025.1561273.

Hyla sarda (Sardinian treefrog) :

2025

Paris, J.R., Bisconti, R., Chiocchio, A., Abueg, L., Absolon, D.E., Tilley, T., Jain, N., Balacco, J., O'Toole, B., Jarvis, E.D., Formenti, G., Salvi, D., Canestrelli, D. :

Chromosome-level genome assembly of the Tyrrhenian tree frog (Hyla sarda). Sci Data 12:1539, 2025. Pubmed reference: 40897714. DOI: 10.1038/s41597-025-05760-9.

Hylobates lar (common gibbon) :

1996

Arnold, N., Stanyon, R., Jauch, A., O'Brien, P., Wienberg, J. :

Identification of complex chromosome rearrangements in the gibbon by fluorescent in situ hybridization (FISH) of a human chromosome 2q specific microlibrary, yeast artificial chromosomes, and reciprocal chromosome painting. Cytogenet Cell Genet 74:80-5, 1996. Pubmed reference: 8893807. DOI: 10.1159/000134387.

Hylobates moloch (silvery gibbon) :

2023

Escalona, M., VanCampen, J., Maurer, N.W., Haukness, M., Okhovat, M., Harris, R.S., Watwood, A., Hartley, G.A., O'Neill, R.J., Medvedev, P., Makova, K.D., Vollmers, C., Carbone, L., Green, R.E. :

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J Hered 114:35-43, 2023. Pubmed reference: 36146896. DOI: 10.1093/jhered/esac043.

Hylobatidae (gibbons) :

2025

Wang, S., Chen, Z., Luo, A., You, X., Kitchener, A.C., Tu, X., Thakur, M., Umapathy, G., Hu, S., Zhang, T., Zhang, Y., Liu, S., Ding, Y., Liu, F., Dai, Q., Feng, X., Li, L., Pan, Y., Zhang, M., Roos, C., Fan, P., Fu, Q., Wu, D.D. :

Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status. Cell , 2025. Pubmed reference: 41205599. DOI: 10.1016/j.cell.2025.10.016.

Hypotaenidia philippensis (buff-banded rail) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

Ictalurus furcatus (blue catfish) :

2023

Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Bao, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B., Simpson, S., Youngblood, R.C., Duke, M.V., Ballard, L., Phillippy, A., Koren, S., Liu, Z. :

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 21:67, 2023. Pubmed reference: 37013528. DOI: 10.1186/s12915-023-01556-8.

Ictalurus punctatus (channel catfish) :

2023

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 21:67, 2023. Pubmed reference: 37013528. DOI: 10.1186/s12915-023-01556-8.

2019

Zhang, S., Zhang, X., Chen, X., Xu, T., Wang, M., Qin, Q., Zhong, L., Jiang, H., Zhu, X., Liu, H., Shao, J., Zhu, Z., Shi, Q., Bian, W., You, X. :

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus). Front Genet 10:251, 2019. Pubmed reference: 30984241. DOI: 10.3389/fgene.2019.00251.

Ilisha elongata (elongate ilisha) :

2025

Liu, B., Niu, X., Zhang, C., Zheng, S., Gao, L., Han, M., Feng, T., Wu, J., Jiang, C., Kang, S., Xu, D., Liu, Y. :

Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata). Sci Data 12:668, 2025. Pubmed reference: 40258812. DOI: 10.1038/s41597-025-04790-7.

Wu, T., Hu, J., Giap, V., Wang, Q., Lu, L., Li, C. :

A chromosome-level genome assembly of the Chinese herring (Ilisha elongata) uncovered its population dynamics and genes related to lipid metabolism. J Hered 116:771-787, 2025. Pubmed reference: 40360201. DOI: 10.1093/jhered/esaf028.

Intellagama lesueurii (Eastern water dragon) :

2024

Powell, D., Jackson, N., Kaur, P., Dudchenko, O., Aiden, E.L., Georges, A., Frère, C.H. :

The genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation. J Hered 116:571-581, 2024. Pubmed reference: 39364696. DOI: 10.1093/jhered/esae054.

Katsuwonus pelamis (skipjack tuna) :

2024

Liang, X., Huang, J., Liu, B., Wu, F., Liu, J., Lu, J. :

A chromosome-level genome assembly of skipjack tuna, Katsuwonus pelamis (Perciformes: Scombridae). Sci Data 11:1405, 2024. Pubmed reference: 39702362. DOI: 10.1038/s41597-024-04280-2.

Kobus ellipsiprymnus (waterbuck) :

2025

Kirkland, C., Wang, X., Canedo-Ribeiro, C., Álvarez-González, L., Weisz, D., Mena, A., St Leger, J., Dudchenko, O., Aiden, E.L., Ruiz-Herrera, A., Heller, R., King, T., Farré, M. :

Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck. bioRxiv , 2025. Pubmed reference: 40166267. DOI: 10.1101/2025.03.19.644014.

Kryptopterus vitreolus (Glass catfish) :

2024

Bian, C., Li, R.H., Ruan, Z.Q., Chen, W.T., Huang, Y., Liu, L.Y., Zhou, H.L., Chong, C.M., Mu, X.D., Shi, Q. :

Chromosome-level genome assembly of the glass catfish (Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype. Zool Res 45:2095-8137(2024)05-1027-10:1027-1036, 2024. Pubmed reference: 39147717. DOI: 10.24272/j.issn.2095-8137.2023.396.

Labeo rohita (rohu) :

2020

Das, P., Sahoo, L., Das, S.P., Bit, A., Joshi, C.G., Kushwaha, B., Kumar, D., Shah, T.M., Hinsu, A.T., Patel, N., Patnaik, S., Agarwal, S., Pandey, M., Srivastava, S., Meher, P.K., Jayasankar, P., Koringa, P.G., Nagpure, N.S., Kumar, R., Singh, M., Iquebal, M.A., Jaiswal, S., Kumar, N., Raza, M., Das Mahapatra, K., Jena, J. :

De novo assembly and genome-wide SNP discovery in rohu carp, Labeo rohita. Front Genet 11:386, 2020. Pubmed reference: 32373166. DOI: 10.3389/fgene.2020.00386.

Lagodon rhomboides (pinfish) :

2024

Eaton, K.M., Krabbenhoft, T.J., Backenstose, N.J.C., Bernal, M.A. :

The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history. G3 (Bethesda) 14:jkae096, 2024. Pubmed reference: 38739549. DOI: 10.1093/g3journal/jkae096.

Lagopus muta (rock ptarmigan) :

2023

Squires, T.E., Rödin-Mörch, P., Formenti, G., Tracey, A., Abueg, L., Brajuka, N., Jarvis, E., Halapi, E.C., Melsted, P., Höglund, J., Magnússon, K.P. :

A chromosome-level genome assembly for the rock ptarmigan (Lagopus muta). G3 (Bethesda) 13:jkad099, 2023. Pubmed reference: 37141262. DOI: 10.1093/g3journal/jkad099.

Lampetra fluviatilis (European river lamprey) :

2025

Tørresen, O.K., Garmann-Aarhus, B., Nam Khang Hoff, S., Jentoft, S., Svensson, M., Schartum, E., Tooming-Klunderud, A., Skage, M., Krabberød, A., Asbjørn Vøllestad, L., Jakobsen, K.S. :

Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri). J Hered :esaf036, 2025. Pubmed reference: 40506799. DOI: 10.1093/jhered/esaf036.

Lampetra planeri (European brook lamprey) :

2025

Tørresen, O.K., Garmann-Aarhus, B., Nam Khang Hoff, S., Jentoft, S., Svensson, M., Schartum, E., Tooming-Klunderud, A., Skage, M., Krabberød, A., Asbjørn Vøllestad, L., Jakobsen, K.S. :

Lamprotornis superbus (superb starling) :

2021

Rubenstein, D.R., Corvelo, A., MacManes, M.D., Maia, R., Narzisi, G., Rousaki, A., Vandenabeele, P., Shawkey, M.D., Solomon, J. :

Feather gene expression elucidates the developmental basis of plumage iridescence in African starlings. J Hered 112:417-429, 2021. Pubmed reference: 33885791. DOI: 10.1093/jhered/esab014.

Larimichthys crocea (large yellow croaker) :

2025

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Xu, S., Liu, Q., Yang, T., Han, Z. :

A telomere-to-telomere genome assembly of the large yellow croaker provides insights into evolution of golden-yellow coloration. J Genet Genomics 52:1401-1412, 2025. Pubmed reference: 40975488. DOI: 10.1016/j.jgg.2025.09.006.

2024

Chen, X., Miao, L., He, Q., Ke, Q., Pu, F., Li, N., Zhou, T., Xu, P. :

Chromosome-level genome assembly for three geographical stocks of large yellow croaker (Larimichthys crocea). Sci Data 11:1364, 2024. Pubmed reference: 39695114. DOI: 10.1038/s41597-024-04126-x.

None

[No authors listed] :

Genomics 117:111075, None. Pubmed reference: 40618937. DOI: 10.1016/j.ygeno.2025.111075.

Larimichthys polyactis (yellow croaker) :

2025

Liu, F., Zhan, W., Guo, D., Ye, T., Lou, B. :

Chromosome-level genome assembly of the small yellow croaker, Larimichthys polyactis (Perciformes: Sciaenidae). Sci Data 12:721, 2025. Pubmed reference: 40307266. DOI: 10.1038/s41597-025-05072-y.

Liu, F., Wang, R., Ye, T., Zhu, J., Guo, D., Zhan, W., Lou, B. :

First development of a 100 K SNP array for small yellow croaker and its application in genomic selection for growth and disease resistance. BMC Genomics , 2025. Pubmed reference: 41286602. DOI: 10.1186/s12864-025-12343-w.

Lateolabrax maculatus :

2024

Sun, Z., Li, S., Liu, Y., Li, W., Liu, K., Cao, X., Lin, J., Wang, H., Wang, Q., Shao, C. :

Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus). Sci Data 11:175, 2024. Pubmed reference: 38326339. DOI: 10.1038/s41597-024-02988-9.

Laterallus jamaicensis :

2023

Hall, L.A., Wang, I.J., Escalona, M., Beraut, E., Sacco, S., Sahasrabudhe, R., Nguyen, O., Toffelmier, E., Shaffer, H.B., Beissinger, S.R. :

Reference genome of the black rail, Laterallus jamaicensis. J Hered 114:436-443, 2023. Pubmed reference: 37119047. DOI: 10.1093/jhered/esad025.

[No authors listed] :

Correction to: Reference genome of the black rail. J Hered 114:585, 2023. Pubmed reference: 37354561. DOI: 10.1093/jhered/esad038.

Lates calcarifer (barramundi perch) :

2025

Zhang, X., Chen, J., Zhou, W., Wen, J., Shi, Q. :

A telomere-to-telomere gap-free genome assembly of the protandrous hermaphrodite Asian seabass (Lates calcarifer). Sci Data 12:1457, 2025. Pubmed reference: 40841804. DOI: 10.1038/s41597-025-05735-w.

Lates japonicus :

2024

Hashiguchi, Y., Mishina, T., Takeshima, H., Nakayama, K., Tanoue, H., Takeshita, N., Takahashi, H. :

Draft genome of akame (Lates japonicus) reveals possible genetic mechanisms for long-term persistence and adaptive evolution with low genetic diversity. Genome Biol Evol 16:evae174, 2024. Pubmed reference: 39109913. DOI: 10.1093/gbe/evae174.

Lathamus discolor (Swift parrot) :

2024

Silver, L.W., Stojanovic, D., Farquharson, K.A., Alexander, L., Peel, E., Belov, K., Hogg, C.J. :

A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor). F1000Res 13:251, 2024. Pubmed reference: 39301273. DOI: 10.12688/f1000research.144352.2.

Laudakia wui (Wuis rock agama) :

2024

Wei, C., Liu, Y., Yang, L., Yang, D., Weng, S. :

High-quality chromosome-scale genome assembly of Laudakia wui (Laudakia, Agamidae). Sci Data 11:1416, 2024. Pubmed reference: 39706843. DOI: 10.1038/s41597-024-04284-y.

Leiocassis longirostris (Chinese longsnout catfish) :

2024

Liu, Y., Zhai, G., Su, J., Gong, Y., Yang, B., Lu, Q., Xi, L., Zheng, Y., Cao, J., Liu, H., Jin, J., Zhang, Z., Yang, Y., Zhu, X., Wang, Z., Gong, G., Mei, J., Yin, Z., Gozlan, R.E., Xie, S., Han, D. :

The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores. Genome Res 34:981-996, 2024. Pubmed reference: 39122473. DOI: 10.1101/gr.278476.123.

Lemur catta (Ring-tailed lemur) :

2022

Palmada-Flores, M., Orkin, J.D., Haase, B., Mountcastle, J., Bertelsen, M.F., Fedrigo, O., Kuderna, L.F.K., Jarvis, E.D., Marques-Bonet, T. :

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta). Gigascience 11:giac026, 2022. Pubmed reference: 35365833. DOI: 10.1093/gigascience/giac026.

Leopardus pardalis (ocelot) :

2025

Foley, N.M., Brookover, E., Tewes, M.E., Murphy, W.J. :

A chromosome-level genome assembly of the Texas ocelot (Leopardus pardalis albescens). J Hered :esaf095, 2025. Pubmed reference: 41222074. DOI: 10.1093/jhered/esaf095.

Lepidochelys kempii (Atlantic ridley) :

2025

Lepidochelys olivacea (Pacific ridley) :

2025

Lepidonotothen larseni (painted notie) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Lepidonotothen squamifrons (grey rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Lepidosiren paradoxa (South American lungfish) :

2024

Schartl, M., Woltering, J.M., Irisarri, I., Du, K., Kneitz, S., Pippel, M., Brown, T., Franchini, P., Li, J., Li, M., Adolfi, M., Winkler, S., de Freitas Sousa, J., Chen, Z., Jacinto, S., Kvon, E.Z., Correa de Oliveira, L.R., Monteiro, E., Baia Amaral, D., Burmester, T., Chalopin, D., Suh, A., Myers, E., Simakov, O., Schneider, I., Meyer, A. :

The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 634:96-103, 2024. Pubmed reference: 39143221. DOI: 10.1038/s41586-024-07830-1.

Lepisosteus osseus (longnose gar) :

2023

Mallik, R., Carlson, K.B., Wcisel, D.J., Fisk, M., Yoder, J.A., Dornburg, A. :

A chromosome level genome assembly of longnose gar, Lepisosteus osseus. G3 (Bethesda) 13:jkad095, 2023. Pubmed reference: 37119803. DOI: 10.1093/g3journal/jkad095.

Leptailurus serval (serval) :

2025

Harris, A.J., Raudsepp, T., Foley, N.M., Warren, W.C., Lyons, L.A., Murphy, W.J. :

Leptobotia elongata (royal clown loach) :

2024

Wen, Z., Wei, X., Chen, J., Li, Y., Zhou, B., Zhang, C., Fu, P., Prathomya, P., Li, R., Lv, Y., Li, Y., Zeng, W., He, Y., Zhou, L., Fan, J., Shi, Q., Zhang, X. :

Chromosome-level genome assemblies of vulnerable male and female elongate loach (Leptobotia elongata). Sci Data 11:924, 2024. Pubmed reference: 39181886. DOI: 10.1038/s41597-024-03789-w.

Leptotyphlops nigroterminus :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Lepus capensis (brown hare) :

2024

Dong, X., Liu, Y., Chen, Y., Ping, X., Ren, Z., Zhang, Y. :

A chromosome-level genome assembly of Cape hare (Lepus capensis). Sci Data 11:1081, 2024. Pubmed reference: 39362891. DOI: 10.1038/s41597-024-03953-2.

Lethrinus nebulosus (spangled emperor) :

2025

Parata, L., Anstiss, L., de Jong, E., Doran, A., Edwards, R.J., Newman, S.J., Payet, S.D., Skepper, C.L., Wakefield, C.B. :

Chromosome-level genome assembly of the spangled emperor, Lethrinus nebulosus (Forsskål 1775). Sci Data 12:435, 2025. Pubmed reference: 40082478. DOI: 10.1038/s41597-025-04690-w.

Leucoraja erinaceus (little skate) :

2023

Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., González-Rajal, Á., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupiáñez, D.G., Rokhsar, D.S., Gómez-Skarmeta, J.L. :

The little skate genome and the evolutionary emergence of wing-like fins. Nature 616:495-503, 2023. Pubmed reference: 37046085. DOI: 10.1038/s41586-023-05868-1.

Lindbergichthys nudifrons (yellowfin notie) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Liparis tanakae :

2025

Chen, Y., Jin, Y., Su, C., Zhang, F., Shan, X. :

An improved chromosomal-scale genome assembly of the Tanaka's snailfish (Liparis tanakae). Sci Data 12:965, 2025. Pubmed reference: 40490471. DOI: 10.1038/s41597-025-05285-1.

Litoria verreauxii :

2025

Wendt, A.S., Brannelly, L. :

Reference genome and reproduction-focused transcriptome for the threatened alpine tree frog (Litoria verreauxii alpina). F1000Res 14:514, 2025. Pubmed reference: 40529633. DOI: 10.12688/f1000research.163701.1.

Lophura swinhoii (Swinhoe's pheasant) :

2024

Xu, X., Wang, C., Xu, C., Yuan, J., Wang, G., Wu, Y., Huang, C., Jing, H., Yang, P., Xu, L., Peng, S., Shan, F., Xia, X., Jin, F., Hou, F., Wang, J., Mi, D., Ren, Y., Liu, Y., Irwin, D.M., Li, X., Chen, W., Li, G. :

Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 24:e13896, 2024. Pubmed reference: 37955396. DOI: 10.1111/1755-0998.13896.

Lorius hypoinochrous (purple-bellied lory) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Loxodonta africana (African savanna elephant) :

2024

Shi, M., Chen, F., Sahu, S.K., Wang, Q., Yang, S., Wang, Z., Chen, J., Liu, H., Hou, Z., Fang, S.G., Lan, T. :

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 11:63, 2024. Pubmed reference: 38212399. DOI: 10.1038/s41597-023-02729-4.

2023

Prado, N.A., Armstrong, E.E., Brown, J.L., Goldenberg, S.Z., Leimgruber, P., Pearson, V.R., Maldonado, J.E., Campana, M.G. :

Lutjanus argentimaculatus (mangrove red snapper) :

2024

Shekhar, M.S., Katneni, V.K., Jangam, A.K., Krishnan, K., Prabhudas, S.K., Jayaraman, R., Angel, J.R.J., Kailasam, M. :

Genome assembly, full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus. Sci Data 11:796, 2024. Pubmed reference: 39025998. DOI: 10.1038/s41597-024-03633-1.

Lutjanus griseus (grey snapper) :

2025

Hildahl, T., Saillant, E. :

A chromosome-anchored reference assembly for the gray snapper, Lutjanus griseus. Mol Biol Rep 52:99, 2025. Pubmed reference: 39751992. DOI: 10.1007/s11033-024-10195-3.

Lycaon pictus (African hunting dog) :

2024

Kliver, S., Kovacic, I., Mak, S., Sinding, M.S., Stagegaard, J., Petersen, B., Nesme, J., Gilbert, M.T.P. :

A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus). J Hered 116:78-87, 2024. Pubmed reference: 39316562. DOI: 10.1093/jhered/esae052.

Lycodes pallidus (pale eelpout) :

2025

Zhang, R., Wang, R., Miao, X., Li, H., Song, P., Li, Y., Lin, L. :

Chromosome-level genome assembly of an Arctic fish species pale eelpout (Lycodes pallidus). Sci Data 12:1187, 2025. Pubmed reference: 40640179. DOI: 10.1038/s41597-025-05385-y.

Lynx canadensis (Canada lynx) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Lynx rufus (bobcat) :

2022

Lin, M., Escalona, M., Sahasrabudhe, R., Nguyen, O., Beraut, E., Buchalski, M.R., Wayne, R.K. :

A reference genome assembly of the bobcat, Lynx rufus. J Hered 113:615-623, 2022. Pubmed reference: 35696092. DOI: 10.1093/jhered/esac031.

Macaca cyclopis (Taiwan macaque) :

2023

Chiu, K.P., Stuart, L., Ooi, H.S., Yu, J., Smith, D.G., Pei, K.J. :

Genome sequencing and application of Taiwanese macaque Macaca cyclopis. Sci Rep 13:11545, 2023. Pubmed reference: 37460589. DOI: 10.1038/s41598-023-38402-4.

Macaca fascicularis (crab-eating macaque) :

2025

Zhang, S., Xu, N., Fu, L., Yang, X., Ma, K., Li, Y., Yang, Z., Li, Z., Feng, Y., Jiang, X., Han, J., Hu, R., Zhang, L., Lian, D., de Gennaro, L., Paparella, A., Ryabov, F., Meng, D., He, Y., Wu, D., Yang, C., Mao, Y., Bian, X., Lu, Y., Antonacci, F., Ventura, M., Shepelev, V.A., Miga, K.H., Alexandrov, I.A., Logsdon, G.A., Phillippy, A.M., Su, B., Zhang, G., Eichler, E.E., Lu, Q., Shi, Y., Sun, Q., Mao, Y. :

Integrated analysis of the complete sequence of a macaque genome. Nature 640:714-721, 2025. Pubmed reference: 40011769. DOI: 10.1038/s41586-025-08596-w.

Macaca mulatta (Rhesus monkey) :

2025

Zhang, S., Xu, N., Lu, Y., Nie, Y., Li, Z., de Gennaro, L., Fu, L., Zhang, Z., Chen, J., Ma, K., Yang, X., Zhang, J., Schmitz, M.T., Antonacci, F., Bakken, T.E., Ventura, M., Phillippy, A.M., Sun, Q., Mao, Y. :

A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias. bioRxiv , 2025. Pubmed reference: 41019632. DOI: 10.1101/2025.08.04.668424.

Ray, K., Mulch, C., Peterson, S.M., Benjamin, S., Gullicksrud, N., Ericsen, A.J., Vallender, E.J., Ferguson, B.M., Wall, J.D., Bimber, B.N. :

Long-read structural variant discovery and targeted short read genotyping enables population scale characterization of structural variation in rhesus macaques. Genome Biol 26:399, 2025. Pubmed reference: 41272845. DOI: 10.1186/s13059-025-03873-3.

2024

Wang, J., Wang, M., Moshiri, A., Harris, R.A., Raveendran, M., Nguyen, T., Kim, S., Young, L., Wang, K., Wiseman, R., O'Connor, D.H., Johnson, Z., Martinez, M., Montague, M.J., Sayers, K., Lyke, M., Vallender, E., Stout, T., Li, Y., Thomasy, S.M., Rogers, J., Chen, R. :

Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun 15:5658, 2024. Pubmed reference: 38969634. DOI: 10.1038/s41467-024-49922-6.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

2022

Rogers, J. :

Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome 33:91-99, 2022. Pubmed reference: 34999909. DOI: 10.1007/s00335-021-09922-z.

Macropodus opercularis (paradise fish) :

2024

Fodor, E., Okendo, J., Szabó, N., Szabó, K., Czimer, D., Tarján-Rácz, A., Szeverényi, I., Low, B.W., Liew, J.H., Koren, S., Rhie, A., Orbán, L., Miklósi, Á., Varga, M., Burgess, S.M. :

The reference genome of Macropodus opercularis (the paradise fish). Sci Data 11:540, 2024. Pubmed reference: 38796485. DOI: 10.1038/s41597-024-03277-1.

2023

Fodor, E., Okendo, J., Szabó, N., Szabó, K., Czimer, D., Tarján-Rácz, A., Szeverényi, I., Low, B.W., Liew, J.H., Koren, S., Rhie, A., Orbán, L., Miklósi, Á., Varga, M., Burgess, S.M. :

The reference genome of the paradise fish (Macropodus opercularis). bioRxiv , 2023. Pubmed reference: 37609174. DOI: 10.1101/2023.08.10.552018.

Macrotis lagotis (bilby) :

2024

Hogg, C.J., Edwards, R.J., Farquharson, K.A., Silver, L.W., Brandies, P., Peel, E., Escalona, M., Jaya, F.R., Thavornkanlapachai, R., Batley, K., Bradford, T.M., Chang, J.K., Chen, Z., Deshpande, N., Dziminski, M., Ewart, K.M., Griffith, O.W., Marin Gual, L., Moon, K.L., Travouillon, K.J., Waters, P., Whittington, C.M., Wilkins, M.R., Helgen, K.M., Lo, N., Ho, S.Y.W., Ruiz Herrera, A., Paltridge, R., Marshall Graves, J.A., Renfree, M., Shapiro, B., Ottewell, K. :

Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8:1776, 2024. Pubmed reference: 39075174. DOI: 10.1038/s41559-024-02519-0.

Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 8:1311-1326, 2024. Pubmed reference: 38945974. DOI: 10.1038/s41559-024-02436-2.

Macrotis leucura (lesser bilby) :

2024

Mandrillus sphinx (mandrill) :

2020

Yin, Y., Yang, T., Liu, H., Huang, Z., Zhang, Y., Song, Y., Wang, W., Guang, X., Sahu, S.K., Kristiansen, K. :

The draft genome of mandrill (Mandrillus sphinx): An Old World monkey. Sci Rep 10:2431, 2020. Pubmed reference: 32051450. DOI: 10.1038/s41598-020-59110-3.

Manidae (pangolins) :

2023

Houck, M.L., Koepfli, K.P., Hains, T., Khan, R., Charter, S.J., Fronczek, J.A., Misuraca, A.C., Kliver, S., Perelman, P.L., Beklemisheva, V., Graphodatsky, A., Luo, S.J., O'Brien, S.J., Lim, N.T., Chin, J.S.C., Guerra, V., Tamazian, G., Omer, A., Weisz, D., Kaemmerer, K., Sturgeon, G., Gaspard, J., Hahn, A., McDonough, M., Garcia-Treviño, I., Gentry, J., Coke, R.L., Janecka, J.E., Harrigan, R.J., Tinsman, J., Smith, T.B., Aiden, E.L., Dudchenko, O. :

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity. Chromosome Res 31:13, 2023. Pubmed reference: 37043058. DOI: 10.1007/s10577-023-09722-y.

Manis javanica (Malayan pangolin) :

2025

Lan, T., Tian, Y., Shi, M., Liu, B., Lin, Y., Xia, Y., Ma, Y., Sahu, S.K., Wang, Q., Li, J., Chen, J., Hou, F., Yin, C., Wang, K., Fu, Y., Que, T., Liu, W., Liu, H., Li, H., Hua, Y. :

Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin. Gigascience 14:giaf003, 2025. Pubmed reference: 39947250. DOI: 10.1093/gigascience/giaf003.

Manis pentadactyla (Chinese pangolin) :

2025

Lan, T., Tian, Y., Shi, M., Liu, B., Lin, Y., Xia, Y., Ma, Y., Sahu, S.K., Wang, Q., Li, J., Chen, J., Hou, F., Yin, C., Wang, K., Fu, Y., Que, T., Liu, W., Liu, H., Li, H., Hua, Y. :

Mareca falcata (falcated duck) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Martes foina (beach marten) :

2025

Tomarovsky, A., Khan, R., Dudchenko, O., Totikov, A., Serdyukova, N.A., Weisz, D., Vorobieva, N.V., Bulyonkova, T., Abramov, A.V., Nie, W., Wang, J., Romanenko, S.A., Proskuryakova, A.A., Cherkasov, N., Ferguson-Smith, M.A., Yang, F., Balanovskaya, E., Gilbert, M.T.P., Graphodatsky, A.S., Aiden, E.L., Powell, R., Koepfli, K.P., Perelman, P.L., Kliver, S. :

Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics. J Hered 116:548-557, 2025. Pubmed reference: 39879552. DOI: 10.1093/jhered/esaf001.

Mastacembelus armatus (zig-zag eel) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Mazama gouazoupira (gray brocket) :

1997

Yang, F., O'Brien, P.C., Wienberg, J., Neitzel, H., Lin, C.C., Ferguson-Smith, M.A. :

Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi). Chromosoma 106:37-43, 1997. Pubmed reference: 9169585. DOI: 10.1007/s004120050222.

Meda fulgida (spikedace) :

2023

Alexandre, N.M., Cameron, A.C., Tian, D., Chatla, K., Kolora, S.R.R., Whiteman, N.K., Turner, T.F., Reinthal, P.N. :

Chromosome-level reference genomes of two imperiled desert fishes: Spikedace (Meda fulgida) and Loach Minnow (Tiaroga cobitis). G3 (Bethesda) 13:jkad157, 2023. Pubmed reference: 37466215. DOI: 10.1093/g3journal/jkad157.

Megalobrama amblycephala (Wuchang bream) :

2021

Liu, H., Chen, C., Lv, M., Liu, N., Hu, Y., Zhang, H., Enbody, E.D., Gao, Z., Andersson, L., Wang, W. :

A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish. Mol Biol Evol 38:4238-4251, 2021. Pubmed reference: 34003267. DOI: 10.1093/molbev/msab152.

Megalobrama skolkovii :

2025

Ding, R., Yu, D., Yang, K., Wu, X., Liu, H. :

Chromosome-level genome assembly and whole-genome resequencing revealed contrasting population genetic differentiation of Black Bream (Megalobrama skolkovii) (Teleostei: Cyprinidae) allopatric and sympatric to its kin species. Ecol Evol 15:e70874, 2025. Pubmed reference: 39844788. DOI: 10.1002/ece3.70874.

Megalobrama terminalis (black Amur bream) :

2024

Liu, K., Xie, N. :

Full-length transcriptome assembly of black amur bream (Megalobrama terminalis) as a reference resource. Mol Biol Rep 51:1101, 2024. Pubmed reference: 39470845. DOI: 10.1007/s11033-024-10056-z.

Megaptera novaeangliae (humpback whale) :

2024

Carminati, M.V., Gashi, V.L., Li, R., Klee, D.J., Padula, S.R., Patel, A.M., Tan, A.D.Y., Mattos, J., Kane, N. :

Novel Megaptera novaeangliae (Humpback whale) haplotype chromosome-level reference genome. Sci Data 11:1113, 2024. Pubmed reference: 39389970. DOI: 10.1038/s41597-024-03922-9.

Megascops albogularis (White-throated screech owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Megascops choliba (Tropical screech owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Megascops ingens :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Megascops kennicottii (western screech-owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Megascops trichopsis :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Megascops watsonii :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Melanitta fusca (white-winged scoter) :

2024

Cádiz, M.I., Tengstedt, A.N.B., Sørensen, I.H., Pedersen, E.S., Fox, A.D., Hansen, M.M. :

Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data. Evol Appl 17:e70008, 2024. Pubmed reference: 39257569. DOI: 10.1111/eva.70008.

Meleagris gallopavo (turkey) :

2025

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2022

Barros, C.P., Derks, M.F.L., Mohr, J., Wood, B.J., Crooijmans, R.P.M.A., Megens, H.J., Bink, M.C.A.M., Groenen, M.A.M. :

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research. Gigascience 12:giad051, 2022. Pubmed reference: 37489751. DOI: 10.1093/gigascience/giad051.

2010

Aslam, ML., Bastiaansen, JW., Crooijmans, RP., Vereijken, A., Megens, HJ., Groenen, MA. :

A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes. BMC Genomics 11:647, 2010. Pubmed reference: 21092123. DOI: 10.1186/1471-2164-11-647.

Dalloul, R.A., Long, J.A., Zimin, A.V., Aslam, L., Beal, K., Blomberg, L.e. .A.n.n., Bouffard, P., Burt, D.W., Crasta, O., Crooijmans, R.P., Cooper, K., Coulombe, R.A., De, S., Delany, M.E., Dodgson, J.B., Dong, J.J., Evans, C., Frederickson, K.M., Flicek, P., Florea, L., Folkerts, O., Groenen, M.A., Harkins, T.T., Herrero, J., Hoffmann, S., Megens, H.J., Jiang, A., de Jong, P., Kaiser, P., Kim, H., Kim, K.W., Kim, S., Langenberger, D., Lee, M.K., Lee, T., Mane, S., Marcais, G., Marz, M., McElroy, A.P., Modise, T., Nefedov, M., Notredame, C., Paton, I.R., Payne, W.S., Pertea, G., Prickett, D., Puiu, D., Qioa, D., Raineri, E., Ruffier, M., Salzberg, S.L., Schatz, M.C., Scheuring, C., Schmidt, C.J., Schroeder, S., Searle, S.M., Smith, E.J., Smith, J., Sonstegard, T.S., Stadler, P.F., Tafer, H., Tu, Z.J., Van Tassell, C.P., Vilella, A.J., Williams, K.P., Yorke, J.A., Zhang, L., Zhang, H.B., Zhang, X., Zhang, Y., Reed, K.M. :

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8, 2010. Pubmed reference: 20838655. DOI: 10.1371/journal.pbio.1000475.

2007

Reed, KM., Chaves, LD., Mendoza, KM. :

An integrated and comparative genetic map of the turkey genome. Cytogenet Genome Res 119:113-26, 2007. Pubmed reference: 18160790. DOI: 10.1159/000109627.

2005

Reed, KM., Chaves, LD., Hall, MK., Knutson, TP., Harry, DE. :

A comparative genetic map of the turkey genome. Cytogenet Genome Res 111:118-27, 2005. Pubmed reference: 16103652. DOI: 10.1159/000086380.

2003

Harry, DE., Zaitlin, D., Marini, PJ., Reed, KM. :

A first-generation map of the turkey genome. Genome 46:914-24, 2003. Pubmed reference: 14608408. DOI: 10.1139/g03-042.

1999

Huang, H.B., Song, Y.Q., Hsel, M., Zahorchak, R., Chiu, J., Teuscher, C., Smith, E.J. :

Development and characterization of genetic mapping resources for the turkey (Meleagris gallopavo) Journal of Heredity 90:240-242, 1999. Pubmed reference: 9987934.

1990

Bitgood, J.J., Somes, R.G. Jr :

Linkage relationships and gene mapping. In "Poultry Breeding and Genetics" (ed. R.D. Crawford), Elsevier, Amsterdam; Chapter 21 :469-495, 1990.

Melopsittacus undulatus (budgerigar) :

2014

Ganapathy, G., Howard, J.T., Ward, J.M., Li, J., Li, B., Li, Y., Xiong, Y., Zhang, Y., Zhou, S., Schwartz, D.C., Schatz, M., Aboukhalil, R., Fedrigo, O., Bukovnik, L., Wang, T., Wray, G., Rasolonjatovo, I., Winer, R., Knight, J.R., Koren, S., Warren, W.C., Zhang, G., Phillippy, A.M., Jarvis, E.D. :

High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience 3:11, 2014. Pubmed reference: 25061512. DOI: 10.1186/2047-217X-3-11.

1986

Ansari, H.A., Takagi, N., Sasaki, M. :

Melospiza melodia (song sparrow) :

2024

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W., Bowie, R.C.K. :

Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery. Genome Biol Evol 16:evae067, 2024. Pubmed reference: 38566597. DOI: 10.1093/gbe/evae067.

Meriones unguiculatus (Mongolian gerbil) :

2024

Guo, Y., Cui, Y., Sun, M., Zhu, X., Zhang, Y., Lu, J., Li, C., Lv, J., Guo, M., Liu, X., Chen, Z., Du, X., Huo, X. :

Establishment and application of a novel genetic detection panel for SNPs in Mongolian gerbils. Genes (Basel) 15:817, 2024. Pubmed reference: 38927752. DOI: 10.3390/genes15060817.

2023

Brekke, T.D., Papadopulos, A.S.T., Julià, E., Fornas, O., Fu, B., Yang, F., de la Fuente, R., Page, J., Baril, T., Hayward, A., Mulley, J.F. :

A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome. Mol Biol Evol 40:msad115, 2023. Pubmed reference: 37183864. DOI: 10.1093/molbev/msad115.

Merluccius merluccius (European hake) :

2025

Martínez, P., Casas, L., Petit-Marty, N., Blanco, A., Carballeda, M., Vilas-Arrondo, N., Gómez-Garrido, J., Cruz, F., Valeiras, J., Alioto, T., Saborido-Rey, F. :

Screening a new European hake (Merluccius merluccius) chromosome-level genome assembly suggests an XX/XY sex determining system driven by the SRY-box transcription factor 3 (sox3). G3 (Bethesda) 15:jkaf127, 2025. Pubmed reference: 40488516. DOI: 10.1093/g3journal/jkaf127.

Mesocricetus auratus (golden hamster) :

2025

Wang, C., Cheng, Z., Miao, J., Xue, X., Dong, Y., Zhao, L., Guo, H., Wang, J., Wang, Z., Lu, S., Fang, G., Peng, Y., Zhai, Y., Zhang, Z., Gao, D., Wang, Z., Wang, P., Zhang, L., Dunmall, L.S.C., Wang, J., Tang, W., Li, X., Ding, Z., Zhao, X., Li, L., Lemoine, N.R., Wang, Z., Tonge, D., Tan, W., Dong, J., Wang, Y. :

Genomic-transcriptomic analysis identifies the Syrian hamster as a superior animal model for human diseases. BMC Genomics 26:286, 2025. Pubmed reference: 40122829. DOI: 10.1186/s12864-025-11393-4.

2022

Lee, Y.Y., Cal-Kayitmazbatir, S., Francey, L.J., Bahiru, M.S., Hayer, K.E., Wu, G., Zeller, M.J., Roberts, R., Speers, J., Koshalek, J., Berres, M.E., Bittman, E.L., Hogenesch, J.B. :

duper is a null mutation of cryptochrome 1 in Syrian hamsters. Proc Natl Acad Sci U S A 119:e2123560119, 2022. Pubmed reference: 35471909. DOI: 10.1073/pnas.2123560119.

1997

Okuizumi, H., Ohsumi, T., Sasaki, N., Imoto, H., Mizuno, Y., Hanami, T., Yamashita, H., Kamiya, M., Takada, S., Kitamura, A., Muramatsu, M., Nishimura, M., Mori, M., Matsuda, Y., Tagaya, O., Okazaki, Y., Hayashizaki, Y. :

Linkage map of syrian hamster with restriction landmark genomic scanning Mammalian Genome 8:121-128, 1997. Pubmed reference: 9060411.

Metatheria (marsupials) :

2024

Silver, L.W., Hogg, C.J., Belov, K. :

Plethora of new marsupial genomes informs our knowledge of marsupial MHC class II. Genome Biol Evol 16:evae156, 2024. Pubmed reference: 39031605. DOI: 10.1093/gbe/evae156.

Micropterus salmoides (largemouth bass) :

2025

Zhu, T., Song, H., Du, J., Lei, C., Tian, J., Wang, C., Dong, C., Li, S. :

Draft genome assembly of the largemouth bass (Micropterus salmoides). BMC Genom Data 26:28, 2025. Pubmed reference: 40234748. DOI: 10.1186/s12863-025-01318-1.

Microstomus kitt (lemon sole) :

2025

Nebenführ, M., Prochotta, D., Nilsson, M.A., de Jong, M.J., Yazici, T.D., Langefeld, F., Muloongo, M., Woköck, H., Jilg, J., Bender, S.C., Zangl, M.M., Ortega Guatame, J.M., Williams, K., Sonnewald, M., Janke, A. :

Chromosome-level genome assembly of the lemon sole, Microstomus kitt (Pleuronectiformes: Pleuronectidae). GigaByte 2025:gigabyte156, 2025. Pubmed reference: 40469543. DOI: 10.46471/gigabyte.156.

Microtus arvalis (Common vole) :

2024

Gouy, A., Wang, X., Kapopoulou, A., Neuenschwander, S., Schmid, E., Excoffier, L., Heckel, G. :

Genomes of Microtus rodents highlight the importance of olfactory and immune systems in their fast radiation. Genome Biol Evol 16:evae233, 2024. Pubmed reference: 39445808. DOI: 10.1093/gbe/evae233.

1996

Gileva, E.A., Liubashevskiĭ, N.M., Starichenko, V.I., Chibiriak, M.V., Romanov, G.N. :

[Hereditary chromosome instability in the common vole (Microtus arvalis) from the region of the Kyshtym nuclear accident--fact or hypothesis?]. Genetika 32:114-9, 1996. Pubmed reference: 8647413.

Microtus californicus (California vole) :

2025

Kozak, K.M., Escalona, M., Linn, I.J., Chumchim, N., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Seligmann, W., Conroy, C.J., Patton, J.L., Bowie, R.C.K., Nachman, M.W. :

A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles. J Hered :esaf067, 2025. Pubmed reference: 40972894. DOI: 10.1093/jhered/esaf067.

Microtus ilaeus (Kazakhstan vole) :

1995

Mazurok, N.A., Rubtsov, N.B., Ovechkina, I.u.I.u., Nesterova, T.B., Zakiian, S.M. :

[High resolution GTG banding and nucleolus organizer regions of chromosomes from the vole Microtus kirgisorum]. Genetika 31:1132-8, 1995. Pubmed reference: 7590219.

Microtus levis (East European vole) :

1995

Mazurok, N.A., Nesterova, T.B., Zakian, S.M. :

High-resolution G-banding of chromosomes in Microtus subarvalis (Rodentia, Arvicolidae). Hereditas 123:47-52, 1995. Pubmed reference: 8598345.

Mirounga angustirostris (Northern elephant seal) :

2025

Rivera, M.G., Escalona, M., Garza, J.C., Miller, C., Beraut, E., Fairbairn, C., Sacco, S., Seligmann, W.E., Sahasrabudhe, R., Nguyen, O., Toffelmier, E., Shaffer, H.B., Costa, D.P., Beltran, R.S., Meyer, R.S. :

Genome assembly and annotation of a deep-diving pinniped, the northern elephant seal (Mirounga angustirostris). J Hered :esaf083, 2025. Pubmed reference: 41147771. DOI: 10.1093/jhered/esaf083.

Monachus monachus (Mediterranean monk seal) :

2025

Nebenführ, M., Hamadou, A.B., Aguilar, A., Borrell, A., Gkafas, G.A., Janke, A. :

Monodelphis domestica (gray short-tailed opossum) :

2007

Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C. :

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167-77, 2007. Pubmed reference: 17495919. DOI: 10.1038/nature05805.

Morone americana (white perch) :

2025

Paris, J.R., Criss, M.A., Walsh, J.L., Obiol, J.F., Murray, C.S., Boone, J.Q., Petersen, A.M. :

Two genomes of the white perch (Morone americana), an ecologically important teleost. J Hered 116:846-853, 2025. Pubmed reference: 40443058. DOI: 10.1093/jhered/esaf034.

Moschus moschiferus (Siberian musk deer) :

2020

Yi, L., Dalai, M., Su, R., Lin, W., Erdenedalai, M., Luvsantseren, B., Chimedtseren, C., Wang, Z., Hasi, S. :

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features. BMC Genomics 21:108, 2020. Pubmed reference: 32005147. DOI: 10.1186/s12864-020-6495-2.

Mugil cephalus (flathead mullet) :

2022

Shekhar, M.S., Katneni, V.K., Jangam, A.K., Krishnan, K., Prabhudas, S.K., Jani Angel, J.R., Sukumaran, K., Kailasam, M., Jena, J. :

First report of chromosome-level genome assembly for flathead grey mullet, Mugil cephalus (Linnaeus, 1758). Front Genet 13:911446, 2022. Pubmed reference: 35783261. DOI: 10.3389/fgene.2022.911446.

Muntiacus crinifrons (black muntjac) :

1995

Yang, F., Carter, N.P., Shi, L., Ferguson-Smith, M.A. :

A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103:642-52, 1995. Pubmed reference: 7587587. DOI: 10.1007/BF00357691.

Muntiacus gongshanensis :

1995

Yang, F., Carter, N.P., Shi, L., Ferguson-Smith, M.A. :

A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103:642-52, 1995. Pubmed reference: 7587587. DOI: 10.1007/BF00357691.

Muntiacus muntjak (muntjak) :

1995

Yang, F., Carter, N.P., Shi, L., Ferguson-Smith, M.A. :

A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103:642-52, 1995. Pubmed reference: 7587587. DOI: 10.1007/BF00357691.

Muntiacus reevesi (Reeves' muntjac) :

1997

Yang, F., O'Brien, P.C., Wienberg, J., Neitzel, H., Lin, C.C., Ferguson-Smith, M.A. :

Chromosomal evolution of the Chinese muntjac (Muntiacus reevesi). Chromosoma 106:37-43, 1997. Pubmed reference: 9169585. DOI: 10.1007/s004120050222.

1995

Yang, F., Carter, N.P., Shi, L., Ferguson-Smith, M.A. :

A comparative study of karyotypes of muntjacs by chromosome painting. Chromosoma 103:642-52, 1995. Pubmed reference: 7587587. DOI: 10.1007/BF00357691.

Muscicapa striata (spotted flycatcher) :

2023

Baudrin, G., Pons, J.M., Bed'Hom, B., Gil, L., Boyer, R., Dusabyinema, Y., Jiguet, F., Fuchs, J. :

A reference genome assembly for the Spotted Flycatcher (Muscicapa striata). Genome Biol Evol 15:evad140, 2023. Pubmed reference: 37506263. DOI: 10.1093/gbe/evad140.

Mustela lutreola (European mink) :

2023

Skorupski, J., Brandes, F., Seebass, C., Festl, W., Śmietana, P., Balacco, J., Jain, N., Tilley, T., Abueg, L., Wood, J., Sims, Y., Formenti, G., Fedrigo, O., Jarvis, E.D. :

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. Int J Mol Sci 24:14816, 2023. Pubmed reference: 37834264. DOI: 10.3390/ijms241914816.

Mustela nigripes (black-footed ferret) :

2023

Kliver, S., Houck, M.L., Perelman, P.L., Totikov, A., Tomarovsky, A., Dudchenko, O., Omer, A.D., Colaric, Z., Weisz, D., Aiden, E.L., Chan, S., Hastie, A., Komissarov, A., Ryder, O.A., Graphodatsky, A., Johnson, W.E., Maldonado, J.E., Pukazhenthi, B.S., Marinari, P.E., Wildt, D.E., Koepfli, K.P. :

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). J Hered 114:539-548, 2023. Pubmed reference: 37249392. DOI: 10.1093/jhered/esad035.

Mycteria americana (wood stork) :

2024

Flamio, R., Ramstad, K.M. :

Chromosome-level genome of the wood stork (Mycteria americana) provides insight into avian chromosome evolution. J Hered 115:230-239, 2024. Pubmed reference: 38079393. DOI: 10.1093/jhered/esad077.

Mylopharyngodon piceus :

2025

Zhang, Y., Shao, Y., Liu, X., Zhong, L., Zhong, Z., Zeng, W., Zhang, J., Cai, W., Li, R. :

Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies. Sci Data 12:145, 2025. Pubmed reference: 39863650. DOI: 10.1038/s41597-025-04421-1.

Myodes glareolus (Bank vole) :

2024

Calamari, Z.T., Song, A., Cohen, E., Akter, M., Das Roy, R., Hallikas, O., Christensen, M.M., Li, P., Marangoni, P., Jernvall, J., Klein, O.D. :

Bank vole genomics links determinate and indeterminate growth of teeth. BMC Genomics 25:1000, 2024. Pubmed reference: 39472825. DOI: 10.1186/s12864-024-10901-2.

Myotis yumanensis :

2024

Curti, J.N., Fraser, D., Escalona, M., Fairbairn, C.W., Sacco, S., Sahasrabudhe, R., Nguyen, O., Seligmann, W., Sudmant, P.H., Toffelmier, E., Vazquez, J.M., Wayne, R., Shaffer, H.B., Buchalski, M.R. :

A genome assembly of the Yuma myotis bat, Myotis yumanensis. J Hered 115:139-148, 2024. Pubmed reference: 37712349. DOI: 10.1093/jhered/esad053.

Myrmecobius fasciatus (numbat) :

2022

Peel, E., Silver, L., Brandies, P., Hayakawa, T., Belov, K., Hogg, C.J. :

Genome assembly of the numbat (Myrmecobius fasciatus), the only termitivorous marsupial. GigaByte 2022:gigabyte47, 2022. Pubmed reference: 36824518. DOI: 10.46471/gigabyte.47.

Naja atra (Chinese cobra) :

2023

Wang, J., Wu, Y., Wang, S., Mu, W., Zeng, W., Chen, X., Jiang, K., Yang, L., Hu, G., He, F. :

The genome assembly and annotation of the Chinese cobra, Naja atra. GigaByte 2023:gigabyte99, 2023. Pubmed reference: 38033372. DOI: 10.46471/gigabyte.99.

Nanger dama (Dama gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

1993

Vassart, M., Greth, A., Durand, V., Cribiu, E.P. :

An unusual Gazella dama karyotype. Ann Genet 36:117-20, 1993. Pubmed reference: 8215217.

Nanger soemmerringii (Soemmerring's gazelle) :

1995

Vassart, M., Séguéla, A., Hayes, H. :

Chromosomal evolution in gazelles. J Hered 86:216-27, 1995. Pubmed reference: 7608514. DOI: 10.1093/oxfordjournals.jhered.a111565.

Natator depressus (flatback sea turtle) :

2025

Natrix maura :

2025

Carranza, S., Fernández-Guiberteau, D., Blasón, L., Tulloch, S., Monteiro, R., Böhne, A., Fernández, R., Escudero, N., Aguilera, L., Gut, M., Alioto, T.S., Câmara Ferreira, F., Gómez-Garrido, J., Cruz, F., Sinha, S., Haggerty, L., Martin, F., Brown, T. :

ERGA-BGE Genome of the viperine water snake (Natrix maura): a key species for evolutionary insights of freshwater snakes. Open Res Eur 5:215, 2025. Pubmed reference: 40980197. DOI: 10.12688/openreseurope.20863.1.

Neodon fuscus (Smokey vole) :

2025

Yang, P., Qu, J., Wang, Y., Xu, Z., Feng, T., Chang, G., Xu, L., Dong, R., Mi, D., Ren, Y., Li, G., Sun, T. :

Chromosome-level genome of Neodon fuscus sheds light on the evolution and plateau adaptation of N. fuscus and Neodon. BMC Genomics 26:554, 2025. Pubmed reference: 40457188. DOI: 10.1186/s12864-025-11709-4.

Neogale vison (American mink) :

2024

Davoudi, P., Do, D.N., Colombo, S., Rathgeber, B., Sargolzaei, M., Plastow, G., Wang, Z., Hu, G., Valipour, S., Miar, Y. :

Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 14:24, 2024. Pubmed reference: 38167844. DOI: 10.1038/s41598-023-50497-3.

Davoudi, P., Do, D.N., Rathgeber, B., Colombo, S., Sargolzaei, M., Plastow, G., Wang, Z., Miar, Y. :

Characterization of runs of homozygosity islands in American mink using whole-genome sequencing data. J Anim Breed Genet 141:507-520, 2024. Pubmed reference: 38389405. DOI: 10.1111/jbg.12859.

2017

Cai, Z., Petersen, B., Sahana, G., Madsen, L.B., Larsen, K., Thomsen, B., Bendixen, C., Lund, M.S., Guldbrandtsen, B., Panitz, F. :

The first draft reference genome of the American mink (Neovison vison). Sci Rep 7:14564, 2017. Pubmed reference: 29109430. DOI: 10.1038/s41598-017-15169-z.

2012

Anistoroaei, R., Nielsen, V., Markakis, M.N., Karlskov-Mortensen, P., Jørgensen, C.B., Christensen, K., Fredholm, M. :

A re-assigned American mink (Neovison vison) map optimal for genome-wide studies. Gene 511:66-72, 2012. Pubmed reference: 22982743. DOI: 10.1016/j.gene.2012.08.033.

2009

Anistoroaei, R., Ansari, S., Farid, A., Benkel, B., Karlskov-Mortensen, P., Christensen, K. :

An extended anchored linkage map and virtual mapping for the American mink genome based on homology to human and dog. Genomics 94:204-10, 2009. Pubmed reference: 19520153. DOI: 10.1016/j.ygeno.2009.05.014.

2007

Anistoroaei, R., Menzorov, A., Serov, O., Farid, A., Christensen, K. :

The first linkage map of the American mink (Mustela vison). Anim Genet 38:384-8, 2007. Pubmed reference: 17596125. DOI: 10.1111/j.1365-2052.2007.01621.x.

1997

Hameister, H., Klett, C., Bruch, J., Dixkens, C., Vogel, W., Christensen, K. :

Zoo-FISH analysis: the American mink (Mustela vison) closely resembles the cat karyotype. Chromosome Res 5:5-11, 1997. Pubmed reference: 9088638. DOI: 10.1023/a:1018433200553.

1989

Isakova, G.K. :

Cytogenetics of Domestic Mink (Mustela-Vison). Cytogenetics of Animals, (ed. Halnan, C.R.E.) :133-149, 1989.

1987

Serov, O.L., Gradov, A.A., Rubtsov, N.B., Zhdanova, N.S., Pack, S.D., Sukoyan, M.A., Mullakandov, M.R., Zakijan, S.M. :

Genetic map of the American mink: gene conservation and organization of chromosomes. Isozymes Curr Top Biol Med Res 15:179-215, 1987. Pubmed reference: 3298154.

Grafodatskiĭ, A.S., Biltueva, L.S. :

[Homology of G-banded mammalian chromosomes]. Genetika 23:93-103, 1987. Pubmed reference: 3469125.

Isakova, G.K. :

[Cytogenetic study of the American mink bred (Mustela vison) bred in mink-breeding farms]. Genetika 23:1097-1103, 1987. Pubmed reference: 3623093.

Neophema chrysogaster (Orange-bellied parrot) :

2025

Silver, L.W., Farquharson, K.A., Peel, E., Gilbert, M.T.P., Belov, K., Morales, H.E., Hogg, C.J. :

Temporal loss of genome-wide and immunogenetic diversity in a near-extinct parrot. Mol Ecol 34:e17746, 2025. Pubmed reference: 40130423. DOI: 10.1111/mec.17746.

Neophocaena asiaeorientalis :

2024

Yin, D., Chen, C., Lin, D., Hua, Z., Ying, C., Zhang, J., Zhao, C., Liu, Y., Cao, Z., Zhang, H., Wang, C., Liang, L., Xu, P., Jian, J., Liu, K. :

Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise. Gigascience 13:giae067, 2024. Pubmed reference: 39283687. DOI: 10.1093/gigascience/giae067.

Neosalanx taihuensis :

2023

Zhou, Y., Zhang, X., Jian, J., Wang, C., Fang, D., Jiang, S., Ren, L., Ge, Y., Wang, H., You, Y., Chen, C. :

Gap-free genome assembly of Salangid icefish Neosalanx taihuensis. Sci Data 10:768, 2023. Pubmed reference: 37925542. DOI: 10.1038/s41597-023-02677-z.

Nesoenas mayeri (pink pigeon) :

2024

Morales, H.E., van Oosterhout, C., Whitford, H., Tatayah, V., Ruhomaun, K., Groombridge, J.J., Gilbert, M.T.P. :

The genome sequence of the Pink Pigeon, Nesoenas mayeri (Prévost, 1843). Wellcome Open Res 9:336, 2024. Pubmed reference: 41278531. DOI: 10.12688/wellcomeopenres.22471.2.

Nestor notabilis (Kea) :

2014

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D.M., Lee, C., Storz, J.F., Antunes, A., Greenwold, M.J., Meredith, R.W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., da Fonseca, R.R., Alfaro-Núñez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J.T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M.V., Hara, E., Smith, J., Farré, M., Narayan, J., Slavov, G., Romanov, M.N., Borges, R., Machado, J.P., Khan, I., Springer, M.S., Gatesy, J., Hoffmann, F.G., Opazo, J.C., Håstad, O., Sawyer, R.H., Kim, H., Kim, K.W., Kim, H.J., Cho, S., Li, N., Huang, Y., Bruford, M.W., Zhan, X., Dixon, A., Bertelsen, M.F., Derryberry, E., Warren, W., Wilson, R.K., Li, S., Ray, D.A., Green, R.E., O'Brien, S.J., Griffin, D., Johnson, W.E., Haussler, D., Ryder, O.A., Willerslev, E., Graves, G.R., Alström, P., Fjeldså, J., Mindell, D.P., Edwards, S.V., Braun, E.L., Rahbek, C., Burt, D.W., Houde, P., Zhang, Y., Yang, H., Wang, J. :

Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311-20, 2014. Pubmed reference: 25504712. DOI: 10.1126/science.1251385.

Nomascus leucogenys (northern white-cheeked gibbon) :

2024

Luo, Z., Jiang, L., Xu, J., Wang, J., Nie, W., Ning, Z., Yang, F. :

Haplotype-phased genome assemblies and annotation of the northern white-cheeked gibbon (Nomascus leucogenys). Sci Data 11:1279, 2024. Pubmed reference: 39587154. DOI: 10.1038/s41597-024-04073-7.

Nothobranchius furzeri (turquoise killifish) :

2025

Johnson, B.D., Ramesh, B., Jones, A.G. :

The genome of the MZM-0403 strain of the African turquoise killifish, Nothobranchius furzeri. G3 (Bethesda) 15:jkaf075, 2025. Pubmed reference: 40194520. DOI: 10.1093/g3journal/jkaf075.

Notiomystis cincta (hihi) :

2024

Tan, H.Z., Scherer, P., Stuart, K.C., Bailey, S., Lee, K.D., Brekke, P., Ewen, J.G., Whibley, A., Santure, A.W. :

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta). Heredity (Edinb) 133:262-275, 2024. Pubmed reference: 39095652. DOI: 10.1038/s41437-024-00711-3.

2023

Bailey, S., Guhlin, J., Senanayake, D.S., Scherer, P., Brekke, P., Ewen, J.G., Santure, A.W., Whibley, A. :

Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics. Mol Ecol Resour 25:e13823, 2023. Pubmed reference: 37332137. DOI: 10.1111/1755-0998.13823.

Notoryctes typhlops (marsupial mole) :

2025

Frankenberg, S.R., Lucas, S., Feigin, C.Y., Doronina, L., Steffen, R., Hartley, G., Grady, P., Menzies, B.R., De Paoli-Iseppi, R., Donnellan, S., Klein, M., Newton, A., Black, J.R., Clark, M., Cooper, S., O'Neill, R., Clark, N., Schmitz, J., Pask, A.J. :

Unearthing the secrets of Australia's most enigmatic and cryptic mammal, the marsupial mole. Sci Adv 11:eado4140, 2025. Pubmed reference: 39742480. DOI: 10.1126/sciadv.ado4140.

Notothenia rossii (marbled rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Numida meleagris (helmeted guineafowl) :

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

2019

Vignal, A., Boitard, S., Thebault, N., Dayo, G.K., Yapi-Gnaore, V., Youssao, I., Berthouly-Salazar, C., Pálinkás-Bodzsár, N., Guémené, D., Thibaud-Nissen, F., Warren, W.C., Tixier-Boichard, M., Rognon, X. :

A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Mol Ecol Resour 19:997-1014, 2019. Pubmed reference: 30945415. DOI: 10.1111/1755-0998.13017.

Nyctalus aviator :

2024

Geng, Y., Liu, Y., Zhang, Y., Gong, L., Han, Y., Huang, Z., Ke, C., Wu, H., Lin, A., Feng, J., Jiang, T. :

A chromosome-level genome assembly of an avivorous bat species (Nyctalus aviator). Sci Data 11:480, 2024. Pubmed reference: 38730001. DOI: 10.1038/s41597-024-03322-z.

Nyctereutes procyonoides (raccoon dog) :

2021

Chueca, L.J., Kochmann, J., Schell, T., Greve, C., Janke, A., Pfenninger, M., Klimpel, S. :

De novo genome assembly of the raccoon dog (Nyctereutes procyonoides). Front Genet 12:658256, 2021. Pubmed reference: 33995489. DOI: 10.3389/fgene.2021.658256.

1991

Wada, M.Y., Lim, Y., Wursterhill, D.H. :

Banded Karyotype of a Wild-Caught Male Korean Raccoon Dog, Nyctereutes-Procyonoides- Koreensis. Genome 34:302-306, 1991.

1987

Wayne, R.K., Nash, W.G., O'Brien, S.J. :

Chromosomal evolution of the Canidae. II. Divergence from the primitive carnivore karyotype. Cytogenet Cell Genet 44:134-41, 1987. Pubmed reference: 3568762. DOI: 10.1159/000132357.

Ward, O.G., Wurster-Hill, D.H., Ratty, F.J., Song, Y. :

Comparative cytogenetics of Chinese and Japanese raccoon dogs, Nyctereutes procyonoides. Cytogenet Cell Genet 45:177-86, 1987. Pubmed reference: 3691184. DOI: 10.1159/000132451.

1984

Yosida, T.H., Wada, M.Y., Ward, O.G., Wurster-Hill, D.H. :

Further studies on the Japanese raccoon dog karyotypes, with special regard to somatic variation of B-chromosomes. Proceedings of the Japan Academy, B 60:17-20, 1984.

Nymphicus hollandicus (cockatiel) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Ochotona princeps (American pika) :

2021

Sjodin, B.M.F., Galbreath, K.E., Lanier, H.C., Russello, M.A. :

Chromosome-level reference genome assembly for the American pika (Ochotona princeps). J Hered 112:549-557, 2021. Pubmed reference: 34036348. DOI: 10.1093/jhered/esab031.

2016

Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :

LaGomiCs-Lagomorph Genomics Consortium: An international collaborative effort for sequencing the genomes of an entire mammalian order. J Hered 107:295-308, 2016. Pubmed reference: 26921276. DOI: 10.1093/jhered/esw010.

Octopus vulgaris (common octopus) :

2023

Destanovik, D., Schultz, D.T., Styfhals, R., Cruz, F., Gómez-Garrido, J., Gut, M., Gut, I., Fiorito, G., Simakov, O., Alioto, T.S., Ponte, G., Seuntjens, E. :

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). G3 (Bethesda) 13:jkad220, 2023. Pubmed reference: 37850903. DOI: 10.1093/g3journal/jkad220.

Odocoileus hemionus (mule deer) :

2025

Hallas, J.M., Capel, S.L.R., Escalona, M., Nguyen, O., Sacco, S., Sahasrabudhe, R., Seligmann, W., Sacks, B.N., Buchalski, M.R. :

A genome assembly for mule deer, Odocoileus hemionus, from southern California. J Hered :esaf082, 2025. Pubmed reference: 41091831. DOI: 10.1093/jhered/esaf082.

Odocoileus virginianus (white-tailed deer) :

2026

Navarro, D., Latch, E.K., Tallon, A.K., Ott-Conn, C.N., DeYoung, R.W., Walsh, D.P., Euclide, P.T., R G, C., Larson, W.A., Seetharam, A.S., Severin, A.J., Reecy, J.M., Hu, Z.L., Cantrell, J.R., Carstensen, M., Caudell, J.N., Killmaster, C.H., Lockwood, M.L., McKinley, W.T., Norton, A.S., Schuler, K.L., Storm, D.J., Sumners, J.A., Walter, W.D., Blanchong, J.A. :

Development of high-throughput genomic resources to inform white-tailed deer population and disease management. Mol Ecol Resour 26:e70085, 2026. Pubmed reference: 41293965. DOI: 10.1111/1755-0998.70085.

2022

London, E.W., Roca, A.L., Novakofski, J.E., Mateus-Pinilla, N.E. :

A de novo chromosome-level genome assembly of the white-tailed deer, Odocoileus virginianus. J Hered 113:479-489, 2022. Pubmed reference: 35511871. DOI: 10.1093/jhered/esac022.

1993

Gripenberg, U., Wessman, M. :

Restriction Endonuclease Staining Profiles in the C- Heterochromatin of Cervidae. Hereditas 118:251-257, 1993.

Odontamblyopus rebecca :

2024

Lü, Z., Yu, Z., Luo, W., Liu, T., Wang, Y., Liu, Y., Liu, J., Liu, B., Gong, L., Liu, L., Li, Y. :

Chromosome-level genome assembly and annotation of eel goby (Odontamblyopus rebecca). Sci Data 11:160, 2024. Pubmed reference: 38307872. DOI: 10.1038/s41597-024-02997-8.

Odontobutis potamophilus :

2017

Zhang, H., Huang, L., Yin, S., Zhang, G., Ding, Y., Zang, X. :

High-density SNP-based genetic map for Odontobutis potamophila. Anim Genet 48:126-127, 2017. Pubmed reference: 27476504. DOI: 10.1111/age.12471.

Oenanthe melanoleuca (Eastern Black-eared Wheatear) :

2023

Peona, V., Palacios-Gimenez, O.M., Lutgen, D., Olsen, R.A., Alaei Kakhki, N., Andriopoulos, P., Bontzorlos, V., Schweizer, M., Suh, A., Burri, R. :

An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca). G3 (Bethesda) 13:jkad088, 2023. Pubmed reference: 37097035. DOI: 10.1093/g3journal/jkad088.

Okapia johnstoni (okapi) :

2022

Winter, S., Coimbra, R.T.F., Helsen, P., Janke, A. :

A Chromosome-Scale Genome Assembly of the Okapi (Okapia johnstoni). J Hered 113:568-576, 2022. Pubmed reference: 35788365. DOI: 10.1093/jhered/esac033.

1996

Vermeesch, J.R., De Meurichy, W., Van Den Berghe, H., Marynen, P., Petit, P. :

Oncorhynchus clarkii henshawi (Lahontan cutthroat trout) :

None

[No authors listed] :

J Hered :esaf050, None. Pubmed reference: 40643203. DOI: 10.1093/jhered/esaf050.

Oncorhynchus clarkii lewisi (westslope cutthroat trout) :

2025

Flores, A.M., Christensen, K.A., Godin, T., Palti, Y., Campbell, M.R., Waldbieser, G.C., Simpson, S.A., Scheffler, B.E., Smith, S.R., Whiteley, A.R., Kovach, R.P., Luikart, G., Boyer, M.C., Kardos, M., Relyea, S., Wells, C., Koop, B.F. :

The genome assembly of the westslope cutthroat trout, Oncorhynchus lewisi, reveals interspecific chromosomal rearrangements with the rainbow trout, Oncorhynchus mykiss. G3 (Bethesda) 15:jkaf064, 2025. Pubmed reference: 40105693. DOI: 10.1093/g3journal/jkaf064.

Oncorhynchus keta (chum salmon) :

2023

Rondeau, E.B., Christensen, K.A., Johnson, H.A., Sakhrani, D., Biagi, C.A., Wetklo, M., Despins, C.A., Leggatt, R.A., Minkley, D.R., Withler, R.E., Beacham, T.D., Koop, B.F., Devlin, R.H. :

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function. G3 (Bethesda) 13:jkad127, 2023. Pubmed reference: 37293843. DOI: 10.1093/g3journal/jkad127.

Oncorhynchus masou (cherry salmon) :

2024

Christensen, K.A., Flores, A.M., Joshi, J., Shibata, K., Fujimoto, T., Koop, B.F., Devlin, R.H. :

Masu salmon species complex relationships and sex chromosomes revealed from analyses of the masu salmon (Oncorhynchus masou masou) genome assembly. G3 (Bethesda) 15:jkae278, 2024. Pubmed reference: 39607719. DOI: 10.1093/g3journal/jkae278.

Oncorhynchus mykiss (rainbow trout) :

2025

Ali, A., Gao, G., Al-Tobasei, R., Youngblood, R.C., Waldbieser, G.C., Scheffler, B.E., Palti, Y., Salem, M. :

Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line. Sci Data 12:345, 2025. Pubmed reference: 40011488. DOI: 10.1038/s41597-025-04693-7.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

2024

Liu, S., Martin, K.E., Snelling, W.M., Long, R., Leeds, T.D., Vallejo, R.L., Wiens, G.D., Palti, Y. :

Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout. G3 (Bethesda) 14:jkae168, 2024. Pubmed reference: 39041837. DOI: 10.1093/g3journal/jkae168.

Salem, M., Al-Tobasei, R., Ali, A., An, L., Wang, Y., Bai, X., Bi, Y., Zhou, H. :

Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution. Gigascience 13:giae092, 2024. Pubmed reference: 39657104. DOI: 10.1093/gigascience/giae092.

2022

Bernard, M., Dehaullon, A., Gao, G., Paul, K., Lagarde, H., Charles, M., Prchal, M., Danon, J., Jaffrelo, L., Poncet, C., Patrice, P., Haffray, P., Quillet, E., Dupont-Nivet, M., Palti, Y., Lallias, D., Phocas, F. :

Development of a high-density 665 K SNP array for rainbow trout genome-wide genotyping. Front Genet 13:941340, 2022. Pubmed reference: 35923696. DOI: 10.3389/fgene.2022.941340.

2021

Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. :

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout. G3 (Bethesda) 11:jkab052, 2021. Pubmed reference: 33616628. DOI: 10.1093/g3journal/jkab052.

2019

Pearse, D.E., Barson, N.J., Nome, T., Gao, G., Campbell, M.A., Abadía-Cardoso, A., Anderson, E.C., Rundio, D.E., Williams, T.H., Naish, K.A., Moen, T., Liu, S., Kent, M., Moser, M., Minkley, D.R., Rondeau, E.B., Brieuc, M.S.O., Sandve, S.R., Miller, M.R., Cedillo, L., Baruch, K., Hernandez, A.G., Ben-Zvi, G., Shem-Tov, D., Barad, O., Kuzishchin, K., Garza, J.C., Lindley, S.T., Koop, B.F., Thorgaard, G.H., Palti, Y., Lien, S. :

Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 3:1731-1742, 2019. Pubmed reference: 31768021. DOI: 10.1038/s41559-019-1044-6.

2015

Palti, Y., Gao, G., Liu, S., Kent, M.P., Lien, S., Miller, M.R., Rexroad, C.E., Moen, T. :

The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout. Mol Ecol Resour 15:662-72, 2015. Pubmed reference: 25294387. DOI: 10.1111/1755-0998.12337.

2014

Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., Alberti, A., Aury, J.M., Louis, A., Dehais, P., Bardou, P., Montfort, J., Klopp, C., Cabau, C., Gaspin, C., Thorgaard, G.H., Boussaha, M., Quillet, E., Guyomard, R., Galiana, D., Bobe, J., Volff, J.N., Genêt, C., Wincker, P., Jaillon, O., Roest Crollius, H., Guiguen, Y. :

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5:3657, 2014. Pubmed reference: 24755649. DOI: 10.1038/ncomms4657.

2012

Guyomard, R., Boussaha, M., Krieg, F., Hervet, C., Quillet, E. :

A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts. BMC Genet 13:15, 2012. Pubmed reference: 22424132. DOI: 10.1186/1471-2156-13-15.

2011

Palti, Y., Genet, C., Luo, M.C., Charlet, A., Gao, G., Hu, Y., Castaño-Sánchez, C., Tabet-Canale, K., Krieg, F., Yao, J., Vallejo, R.L., Rexroad, C.E. :

A first generation integrated map of the rainbow trout genome. BMC Genomics 12:180, 2011. Pubmed reference: 21473775. DOI: 10.1186/1471-2164-12-180.

2009

Phillips, R.B., Keatley, K.A., Morasch, M.R., Ventura, A.B., Lubieniecki, K.P., Koop, B.F., Danzmann, R.G., Davidson, W.S. :

Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss). BMC Genet 10:46, 2009. Pubmed reference: 19689812. DOI: 10.1186/1471-2156-10-46.

2006

Guyomard, R., Mauger, S., Tabet-Canale, K., Martineau, S., Genet, C., Krieg, F., Quillet, E. :

A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7:302, 2006. Pubmed reference: 17137492. DOI: 10.1186/1471-2164-7-302.

2000

Sakamoto, T., Danzmann, R.G., Gharbi, K., Howard, P., Ozaki, A., Khoo, S.K., Woram, R.A., Okamoto, N., Ferguson, M.M., Holm, L.E., Guyomard, R., Hoyheim, B. :

A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates Genetics 155:1331-1345, 2000. Pubmed reference: 10880492.

1998

Young, W.P., Wheeler, P.A., Coryell, V.H., Keim, P., Thorgaard, G.H. :

A detailed linkage map of rainbow trout produced using doubled haploids Genetics 148:839-850, 1998. Pubmed reference: 9504929.

1988

Lloyd, M.A., Thorgaard, G.H. :

Restriction endonuclease banding of rainbow trout chromosomes. Chromosoma 96:171-177, 1988.

Oncorhynchus nerka (sockeye salmon) :

2012

Everett, M.V., Miller, M.R., Seeb, J.E. :

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing. BMC Genomics 13:521, 2012. Pubmed reference: 23031582. DOI: 10.1186/1471-2164-13-521.

Oplegnathus fasciatus (barred knifejaw) :

2021

Bai, Y., Gong, J., Zhou, Z., Li, B., Zhao, J., Ke, Q., Zou, X., Pu, F., Wu, L., Zheng, W., Zhou, T., Xu, P. :

Chromosome-level assembly of the Southern Rock Bream (Oplegnathus fasciatus) genome using PacBio and Hi-C technologies. Front Genet 12:811798, 2021. Pubmed reference: 34992639. DOI: 10.3389/fgene.2021.811798.

Opsanus beta (Gulf toadfish) :

2024

Kron, N.S., Young, B.D., Drown, M.K., McDonald, M.D. :

Long-read de novo genome assembly of Gulf toadfish (Opsanus beta). BMC Genomics 25:871, 2024. Pubmed reference: 39289604. DOI: 10.1186/s12864-024-10747-8.

Opsariichthys bidens :

2025

Wang, X., Liu, Q., Yin, D., Wang, P., Jiang, M., Liu, J., Sun, N., Yan, Y., Liu, K. :

Telomere-to-telomere gap-free genome assembly and comparative analysis of the Opsariichthys bidens (Cypriniformes: Xenocyprididae). Biology (Basel) 14:1544, 2025. Pubmed reference: 41300333. DOI: 10.3390/biology14111544.

Orcinus orca (killer whale) :

2023

Foote, A.D., Alexander, A., Ballance, L.T., Constantine, R., Galletti Vernazzani Muñoz, B., Guinet, C., Robertson, K.M., Sinding, M.S., Sironi, M., Tixier, P., Totterdell, J., Towers, J.R., Wellard, R., Pitman, R.L., Morin, P.A. :

"Type D" killer whale genomes reveal long-term small population size and low genetic diversity. J Hered 114:94-109, 2023. Pubmed reference: 36971118. DOI: 10.1093/jhered/esac070.

Oreochromis mossambicus (Mozambique tilapia) :

2021

Tao, W., Cao, J., Xiao, H., Zhu, X., Dong, J., Kocher, T.D., Lu, M., Wang, D. :

A chromosome-level genome assembly of Mozambique tilapia (Oreochromis mossambicus) reveals the structure of sex determining regions. Front Genet 12:796211, 2021. Pubmed reference: 34956335. DOI: 10.3389/fgene.2021.796211.

Oreochromis mossambicus x niloticus :

2022

Etherington, G.J., Nash, W., Ciezarek, A., Mehta, T.K., Barria, A., Peñaloza, C., Khan, M.G.Q., Durrant, A., Forrester, N., Fraser, F., Irish, N., Kaithakottil, G.G., Lipscombe, J., Trong, T., Watkins, C., Swarbreck, D., Angiolini, E., Cnaani, A., Gharbi, K., Houston, R.D., Benzie, J.A.H., Haerty, W. :

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics 23:832, 2022. Pubmed reference: 36522771. DOI: 10.1186/s12864-022-09065-8.

Oreochromis niloticus (Nile tilapia) :

2025

Etherington, G., Ciezarek, A., Mehta, T., Barker, T., Durrant, A., Fraser, F., Henderson, S., Irish, N., Kaithakottil, G., Knitlhoffer, V., Ali, S., Trong, T., Watkins, C., Swarbreck, D., Gharbi, K., Benzie, J., Haerty, W. :

Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly. Sci Rep 15:16057, 2025. Pubmed reference: 40341759. DOI: 10.1038/s41598-025-01300-y.

2011

Lee, B.Y., Coutanceau, J.P., Ozouf-Costaz, C., D'Cotta, H., Baroiller, J.F., Kocher, T.D. :

Genetic and physical mapping of sex-linked AFLP markers in Nile tilapia (Oreochromis niloticus). Mar Biotechnol (NY) 13:557-62, 2011. Pubmed reference: 20953654. DOI: 10.1007/s10126-010-9326-7.

2005

Lee, B.Y., Lee, W.J., Streelman, J.T., Carleton, K.L., Howe, A.E., Hulata, G., Slettan, A., Stern, J.E., Terai, Y., Kocher, T.D. :

A second-generation genetic linkage map of tilapia (Oreochromis spp.). Genetics 170:237-44, 2005. Pubmed reference: 15716505. DOI: 10.1534/genetics.104.035022.

2004

Ezaz, M.T., Harvey, S.C., Boonphakdee, C., Teale, A.J., McAndrew, B.J., Penman, D.J. :

Isolation and physical mapping of sex-linked AFLP markers in nile tilapia (Oreochromis niloticus L.). Mar Biotechnol (NY) 6:435-45, 2004. Pubmed reference: 15791488. DOI: 10.1007/s10126-004-3004-6.

2000

McConnell, S.K., Beynon, C., Leamon, J., Skibinski, D.O. :

Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed. Anim Genet 31:214-8, 2000. Pubmed reference: 10895314.

1998

Kocher, T.D., Lee, W.J., Sobolewska, H., Penman, D., McAndrew, B. :

A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics 148:1225-32, 1998. Pubmed reference: 9539437.

Orientallactaga sibirica (Mongolian five-toed jerboa) :

2024

Chai, S., Chong, Y., Yin, D., Qiu, Q., Xu, S., Yang, G. :

Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. Sci China Life Sci 67:2003-2015, 2024. Pubmed reference: 38902451. DOI: 10.1007/s11427-023-2516-9.

Ornithorhynchus anatinus (platypus) :

2025

Gonsalvez, A., Peel, E., Hogg, C.J., Belov, K. :

Insights into platypus crural gland transcriptomics - venom and beyond. BMC Genomics , 2025. Pubmed reference: 41257598. DOI: 10.1186/s12864-025-12299-x.

2021

Zhou, Y., Shearwin-Whyatt, L., Li, J., Song, Z., Hayakawa, T., Stevens, D., Fenelon, J.C., Peel, E., Cheng, Y., Pajpach, F., Bradley, N., Suzuki, H., Nikaido, M., Damas, J., Daish, T., Perry, T., Zhu, Z., Geng, Y., Rhie, A., Sims, Y., Wood, J., Haase, B., Mountcastle, J., Fedrigo, O., Li, Q., Yang, H., Wang, J., Johnston, S.D., Phillippy, A.M., Howe, K., Jarvis, E.D., Ryder, O.A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H.A., Graves, J., Belov, K., Renfree, M.B., Grutzner, F., Zhou, Q., Zhang, G. :

Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592:756-762, 2021. Pubmed reference: 33408411. DOI: 10.1038/s41586-020-03039-0.

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2018

Martin, H.C., Batty, E.M., Hussin, J., Westall, P., Daish, T., Kolomyjec, S., Piazza, P., Bowden, R., Hawkins, M., Grant, T., Moritz, C., Grutzner, F., Gongora, J., Donnelly, P. :

Insights into Platypus Population Structure and History from Whole-Genome Sequencing. Mol Biol Evol 35:1238-1252, 2018. Pubmed reference: 29688544. DOI: 10.1093/molbev/msy041.

Orycteropus afer (aardvark) :

2003

Yang, F., Alkalaeva, E.Z., Perelman, P.L., Pardini, A.T., Harrison, W.R., O'Brien, P.C., Fu, B., Graphodatsky, A.S., Ferguson-Smith, M.A., Robinson, T.J. :

Oryctolagus cuniculus (rabbit) :

2025

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Chen, X., Yu, C., Liu, D., Zhong, Q., Zhou, J., Lin, W., Yang, Y., Xie, J., Wang, X., Wu, S., Qian, L., Lin, Y., Xie, X., Huang, Z. :

Near telomere to telomere genome assembly of Chinese yellow rabbit (Oryctolagus cuniculus). Sci Data 12:1786, 2025. Pubmed reference: 41233384. DOI: 10.1038/s41597-025-06058-6.

2024

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

2023

Ballan, M., Bovo, S., Bertolini, F., Schiavo, G., Schiavitto, M., Negrini, R., Fontanesi, L. :

Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds. J Anim Breed Genet 140:663-678, 2023. Pubmed reference: 37435689. DOI: 10.1111/jbg.12818.

2021

Yang, N., Zhao, B., Chen, Y., D'Alessandro, E., Chen, C., Ji, T., Wu, X., Song, C. :

Distinct retrotransposon evolution profile in the genome of rabbit (Oryctolagus cuniculus). Genome Biol Evol 13:evab168, 2021. Pubmed reference: 34270728. DOI: 10.1093/gbe/evab168.

2018

Zhou, L., Xiao, Q., Bi, J., Wang, Z., Li, Y. :

RabGTD: a comprehensive database of rabbit genome and transcriptome. Database (Oxford) 2018:bay075, 2018. Pubmed reference: 30010730. DOI: 10.1093/database/bay075.

2016

Fontanesi, L., Di Palma, F., Flicek, P., Smith, A.T., Thulin, C.G., Alves, P.C. :

2015

Sternstein, I., Reissmann, M., Maj, D., Bieniek, J., Brockmann, G.A. :

A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits. BMC Genet 16:16, 2015. Pubmed reference: 25887754. DOI: 10.1186/s12863-015-0168-1.

2014

Carneiro, M., Rubin, C.J., Di Palma, F., Albert, F.W., Alföldi, J., Martinez Barrio, A., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J.M., Barrell, D., Bolet, G., Boucher, S., Burbano, H.A., Campos, R., Chang, J.L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R.G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J.M., Lander, E.S., Ferrand, N., Lindblad-Toh, K., Andersson, L. :

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345:1074-1079, 2014. Pubmed reference: 25170157. DOI: 10.1126/science.1253714.

Lohmueller, K.E. :

Evolution. On the origin of Peter Rabbit. Science 345:1000-1, 2014. Pubmed reference: 25170135. DOI: 10.1126/science.1258775.

2012

Fontanesi, L., Martelli, P.L., Scotti, E., Russo, V., Rogel-Gaillard, C., Casadio, R., Vernesi, C. :

Exploring copy number variation in the rabbit (Oryctolagus cuniculus) genome by array comparative genome hybridization. Genomics 100:245-51, 2012. Pubmed reference: 22800765. DOI: 10.1016/j.ygeno.2012.07.001.

1997

Kumarasamy, P., Thangaraju, P., Nainar, A.M. :

Karyological studies in domestic rabbits (oryctolagus cuniculus). Indian Journal of Animal Sciences 67:1007-1009, 1997.

1991

Poulsen, B.S., Kristiansen, K., Rønne, M. :

Comparative analysis of autosomes in karyotypes from pig and rabbit using RBG-banding and in situ hybridization. Cytobios 67:23-7, 1991. Pubmed reference: 1935256.

Poulsen, B.S., Ronne, M. :

High-Resolution R-Banding and Localization of Fragile Sites in Oryctolagus-Cuniculus. Genetics Selection Evolution 23:S183-S186, 1991.

1989

Yerle, M., Echard, G. :

High Resolution Gtg Banding Pattern of Rabbit Chromosomes. Cytogenetics of Animals, (ed. Halnan, C.R.E.) :301-304, 1989.

1988

Poulsen, B.S., Shibasaki, Y., Rønne, M. :

The high resolution R-banded karyotype of Oryctolagus cuniculus L. Hereditas 109:57-60, 1988. Pubmed reference: 3192427. DOI: 10.1111/j.1601-5223.1988.tb00182.x.

1987

Grafodatskiĭ, A.S., Biltueva, L.S. :

[Homology of G-banded mammalian chromosomes]. Genetika 23:93-103, 1987. Pubmed reference: 3469125.

Yerle, M., Echard, G., Gillois, M. :

The high-resolution GTG-banding pattern of rabbit chromosomes. Cytogenet Cell Genet 45:5-9, 1987. Pubmed reference: 3595212. DOI: 10.1159/000132416.

1983

Soulié, J., de Grouchy, J. :

New gene assignments in the rabbit (Oryctolagus cuniculus). Comparison with other species. Hum Genet 63:48-52, 1983. Pubmed reference: 6572613. DOI: 10.1007/BF00285397.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1963

Sharma, G.P., Parshad, R., Ghuman, S.K. :

On the meiotic and somatic chromosomes of the rabbit, Oryctolagus culniculus. Research Bulletin of the Panjab University of Science 14:171-173, 1963.

1941

Castle, W.E., Sawin, P.B. :

Genetic linkage in the rabbit. Proc Natl Acad Sci U S A 27:519-23, 1941. Pubmed reference: 16588495. DOI: 10.1073/pnas.27.11.519.

1936

Castle, W.E. :

Further Data on Linkage in Rabbits. Proc Natl Acad Sci U S A 22:222-5, 1936. Pubmed reference: 16577699. DOI: 10.1073/pnas.22.4.222.

Oryx dammah (scimitar-horned oryx) :

1994

Claro, F., Hayes, H., Cribiu, E.P. :

The C-, G-, and R-banded karyotype of the scimitar-horned oryx (Oryx dammah). Hereditas 120:1-6, 1994. Pubmed reference: 8206781. DOI: 10.1111/j.1601-5223.1994.00001.x.

Oryx leucoryx (Arabian oryx) :

1989

Cribiu, E.P., Durand, V., Asmodé, J.F., Greth, A., Anagariyah, S. :

The G- and C-banding karyotype of the Arabian oryx (Oryx leucoryx). Ann Genet 32:200-3, 1989. Pubmed reference: 2610485.

Oryzias latipes (Japanese medaka) :

2025

Morikami, K., Tanizawa, Y., Yagura, M., Sakamoto, M., Kawamoto, S., Nakamura, Y., Yamaguchi, K., Shigenobu, S., Naruse, K., Ansai, S., Kuraku, S. :

MedakaBase as a unified genomic resource platform for medaka fish biology. DNA Res :dsaf030, 2025. Pubmed reference: 41122912. DOI: 10.1093/dnares/dsaf030.

1999

Ohtsuka, M., Makino, S., Yoda, K., Wada, H., Naruse, K., Mitani, H., Shima, A., Ozato, K., Kimura, M., Inoko, H. :

Construction of a linkage map of the medaka (Oryzias latipes) and mapping of the Da mutant locus defective in dorsoventral patterning Genome Research 9:1277-1287, 1999. Pubmed reference: 10613850.

Oryzias melastigma (Indian medaka) :

2025

Kim, M.S., Lee, J.S., Kim, D.H., Park, J.J.C., Sayed, A.E.H., Zhu, X., Wang, Y., Wang, M., Yang, Z., Lee, J.S. :

Chromosome-level genome assembly of the marine medaka (Oryzias melastigma) using Hi-C technology: Genomic analysis and profiling of DNA methylation for epigenetic study. Comp Biochem Physiol Part D Genomics Proteomics 56:S1744-117X(25)00169-8:101580, 2025. Pubmed reference: 40749602. DOI: 10.1016/j.cbd.2025.101580.

2020

Liang, P., Saqib, H.S.A., Ni, X., Shen, Y. :

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). BMC Genomics 21:640, 2020. Pubmed reference: 32938378. DOI: 10.1186/s12864-020-07042-7.

Oryzias sinensis (Chinese medaka) :

2024

Dong, Z., Wang, J., Chen, G., Guo, Y., Zhao, N., Wang, Z., Zhang, B. :

A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis. Sci Data 11:322, 2024. Pubmed reference: 38548787. DOI: 10.1038/s41597-024-03173-8.

Osteoglossum bicirrhosum (silver arawana) :

2025

Liu, Y., Bian, C., Ma, K.Y., Yang, Y., Wang, Y., Liu, C., Ouyang, G., Xu, M., Sun, J., Shao, C., Chen, J., Shi, Q., Mu, X. :

Reference genome provide insights into sex determination of silver aworana (Osteoglossum bicirrhosum). BMC Biol 23:29, 2025. Pubmed reference: 39875888. DOI: 10.1186/s12915-025-02139-5.

Ostrea denselamellosa :

2023

Dong, Z., Bai, Y., Liu, S., Yu, H., Kong, L., Du, S., Li, Q. :

A chromosome-level genome assembly of Ostrea denselamellosa provides initial insights into its evolution. Genomics 115:110582, 2023. Pubmed reference: 36796653. DOI: 10.1016/j.ygeno.2023.110582.

Otis tarda (great bustard) :

2023

Luo, H., Jiang, X., Li, B., Wu, J., Shen, J., Xu, Z., Zhou, X., Hou, M., Huang, Z., Ou, X., Xu, L. :

A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes). Commun Biol 6:746, 2023. Pubmed reference: 37463976. DOI: 10.1038/s42003-023-05137-x.

Otocolobus manul (Pallas's cat) :

2024

Bubenikova, J., Plasil, M., Burger, P.A., Horin, P. :

Four new genome sequences of the Pallas's cat (Otocolobus manul): an insight into the patterns of within-species variability. Front Genet 15:1463774, 2024. Pubmed reference: 39720181. DOI: 10.3389/fgene.2024.1463774.

2023

Flack, N., Drown, M., Walls, C., Pratte, J., McLain, A., Faulk, C. :

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 5:lqad033, 2023. Pubmed reference: 37025970. DOI: 10.1093/nargab/lqad033.

Otospermophilus beecheyi (California ground squirrel) :

None

[No authors listed] :

J Hered :esaf045, None. Pubmed reference: 40600666. DOI: 10.1093/jhered/esaf045.

Otus brucei (pallid scops owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus elegans (elegant scops-owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus icterorhynchus :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus lempiji (sunda scops owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus lettia (collared scops owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus longicornis :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus manadensis :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus mirus :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus nigrorum (Negros scops owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus rutilus :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus scops (Eurasian scops-owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus semitorques (Japanese scops-owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Otus senegalensis :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Ovibos moschatus (muskox) :

2024

Lok, S., Lau, T.N.H., Trost, B., Tong, A.H.Y., Paton, T., Wintle, R.F., Engstrom, M.D., Gunn, A., Scherer, S.W. :

Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics. Sci Rep 14:21023, 2024. Pubmed reference: 39284808. DOI: 10.1038/s41598-024-67270-9.

2023

Li, M., Li, X., Wu, Z., Zhang, G., Wang, N., Dou, M., Liu, S., Yang, C., Meng, G., Sun, H., Hvilsom, C., Xie, G., Li, Y., Li, Z.H., Wang, W., Jiang, Y., Heller, R., Wang, Y. :

Convergent molecular evolution of thermogenesis and circadian rhythm in Arctic ruminants. Proc Biol Sci 290:20230538, 2023. Pubmed reference: 37253422. DOI: 10.1098/rspb.2023.0538.

1995

Biltueva, L.S., Sharshov, A.A., Graphodatsky, A.S. :

G-banding homologies in musk ox, ovibos moschatus, and other bovids. Hereditas 122:185-187, 1995.

1994

Pasitschniak-Arts, M., Flood, P.F., Schmutz, S.M., Seidel, B. :

Ovis ammon (argali) :

2025

Wang, M.Y., Zhang, B.L., Liang, Q.Q., Lian, X.M., Zhang, K., Yang, Q.E., Yang, W.K. :

Chromosome-level genome assembly, annotation, and population genomic resource of argali (Ovis ammon). Sci Data 12:57, 2025. Pubmed reference: 39799149. DOI: 10.1038/s41597-025-04400-6.

1990

Bunch, T.D., Mitchell, R.M., Maciulis, A. :

G-Banded Chromosomes of the Gansu Argali (Ovis-Ammon-Jubata) and Their Implications in the Evolution of the Ovis Karyotype. Journal of Heredity 81:227-230, 1990.

Ovis aries (sheep) :

2025

Luo, L.Y., Wu, H., Zhao, L.M., Zhang, Y.H., Huang, J.H., Liu, Q.Y., Wang, H.T., Mo, D.X., EEr, H.H., Zhang, L.Q., Chen, H.L., Jia, S.G., Wang, W.M., Li, M.H. :

Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness. Nat Genet 57:218-230, 2025. Pubmed reference: 39779954. DOI: 10.1038/s41588-024-02037-6.

Gou, Y., Jing, Y., Wang, Y., Li, X., Yang, J., Wang, K., He, H., Yang, Y., Tang, Y., Wang, C., Xu, J., Yang, F., Li, M., Tang, Q. :

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Zhao, B., Luo, H., Fu, X., Zhang, G., Clark, E.L., Wang, F., Dalrymple, B.P., Oddy, V.H., Vercoe, P.E., Wu, C., Liu, G.E., Li, C.J., Xiang, R., Tian, K., Zhang, Y., Fang, L. :

A developmental gene expression atlas reveals novel biological basis of complex phenotypes in sheep. Genomics Proteomics Bioinformatics 23:qzaf020, 2025. Pubmed reference: 40037845. DOI: 10.1093/gpbjnl/qzaf020.

Liu, J., Mo, D., Luo, L., Shi, Y., Xu, S. :

Sheep pan-genome retrieves the lost sequences and genes during domestication and selection. Genomics 117:S0888-7543(25)00063-1:111047, 2025. Pubmed reference: 40258447. DOI: 10.1016/j.ygeno.2025.111047.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Nesengani, L.T., Tshilate, T., Mdyogolo, S., Smith, R., Masebe, T., Raphulu, T., Moila, A., Sharaf, A., Muzemil, S., Houaga, I., Muigai, A., Djikeng, A., Kuja, J., Katee, S., Osuji, J.O., Mungloo-Dilmohamud, Z., Botes, M., Mbizeni, S., Jarvis, E., Ebenezer, T.E., Ntanganedzeni, M. :

A chromosomal level genome assembly of Nguni Sheep, Ovis aries. Sci Data 12:1193, 2025. Pubmed reference: 40640211. DOI: 10.1038/s41597-025-05514-7.

Xiang, X., Guo, Y., Zhao, L., Gao, W., Li, M., Zhao, P., Wang, Z. :

Whole genome sequencing and structural variations provide insights into the body size traits of Hu sheep. Sci Data 12:1373, 2025. Pubmed reference: 40770274. DOI: 10.1038/s41597-025-05734-x.

Kantanen, J., Weldenegodguad, M., Pokharel, K. :

Oar_Finn: the genome assembly and annotation of an exceptionally fertile Finnsheep (Ovis aries) Ewe. BMC Genom Data 26:59, 2025. Pubmed reference: 40826014. DOI: 10.1186/s12863-025-01354-x.

Zhong, C., Zhang, L., Song, W., Guo, Y., Liu, J., Baqian, Z., Wang, J., Li, R., Su, J. :

Genome assembly and whole-genome resequencing study of Butuo Black sheep (Ovis aries). Sci Data 12:1725, 2025. Pubmed reference: 41173846. DOI: 10.1038/s41597-025-05805-z.

2024

Qiao, G., Xu, P., Guo, T., He, X., Yue, Y., Yang, B. :

Genome-wide detection of structural variation in some sheep breeds using whole-genome long-read sequencing data. J Anim Breed Genet 141:403-414, 2024. Pubmed reference: 38247268. DOI: 10.1111/jbg.12846.

Li, M., Lu, Y., Gao, Z., Yue, D., Hong, J., Wu, J., Xi, D., Deng, W., Chong, Y. :

Pan-Omics in sheep: Unveiling genetic landscapes. Animals (Basel) 14:273, 2024. Pubmed reference: 38254442. DOI: 10.3390/ani14020273.

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 11:488, 2024. Pubmed reference: 38734729. DOI: 10.1038/s41597-024-03338-5.

Lu, Z., Yuan, C., An, X., Chen, Z., Guo, T., Liu, J. :

Chromosome-level genome assembly of Guide Black-Fur sheep (Ovis aries). Sci Data 11:711, 2024. Pubmed reference: 38951548. DOI: 10.1038/s41597-024-03564-x.

You, X., Fang, Q., Chen, C., Cao, J., Fu, S., Zhang, T., Wang, S., He, X., He, J., Zhou, Y., Wang, B., Wang, L., Wang, Z., Sun, T., Yang, X., Te, R., Jian, J., Zhou, H., Dai, Y., Liu, Y. :

A near complete genome assembly of the East Friesian sheep genome. Sci Data 11:762, 2024. Pubmed reference: 38992134. DOI: 10.1038/s41597-024-03581-w.

You, X., Fang, Q., Chen, C., Cao, J., Fu, S., Zhang, T., Wang, S., He, X., He, J., Zhou, Y., Wang, B., Wang, L., Wang, Z., Sun, T., Yang, X., Te, R., Jian, J., Zhou, H., Dai, Y., Liu, Y. :

Author Correction: A near complete genome assembly of the East Friesian sheep genome. Sci Data 11:947, 2024. Pubmed reference: 39209856. DOI: 10.1038/s41597-024-03755-6.

Zhang, D., Cheng, J., Li, X., Huang, K., Yuan, L., Zhao, Y., Xu, D., Zhang, Y., Zhao, L., Yang, X., Ma, Z., Xu, Q., Li, C., Wang, X., Zheng, C., Tang, D., Nian, F., Yue, X., Li, W., Tian, H., Weng, X., Hu, P., Feng, Y., Kalds, P., Jiang, Z., Zhao, Y., Zhang, X., Li, F., Wang, W. :

Comprehensive multi-tissue epigenome atlas in sheep: A resource for complex traits, domestication, and breeding. Imeta 3:e254, 2024. Pubmed reference: 39742295. DOI: 10.1002/imt2.254.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Li, R., Gong, M., Zhang, X., Wang, F., Liu, Z., Zhang, L., Yang, Q., Xu, Y., Xu, M., Zhang, H., Zhang, Y., Dai, X., Gao, Y., Zhang, Z., Fang, W., Yang, Y., Fu, W., Cao, C., Yang, P., Ghanatsaman, Z.A., Negari, N.J., Nanaei, H.A., Yue, X., Song, Y., Lan, X., Deng, W., Wang, X., Pan, C., Xiang, R., Ibeagha-Awemu, E.M., Heslop-Harrison, P.J.S., Rosen, B.D., Lenstra, J.A., Gan, S., Jiang, Y. :

A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res 33:463-477, 2023. Pubmed reference: 37310928. DOI: 10.1101/gr.277372.122.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Woolley, S.A., Salavati, M., Clark, E.L. :

Recent advances in the genomic resources for sheep. Mamm Genome 34:545-558, 2023. Pubmed reference: 37752302. DOI: 10.1007/s00335-023-10018-z.

Xie, S., Isaacs, K., Becker, G., Murdoch, B.M. :

A computational framework for improving genetic variants identification from 5,061 sheep sequencing data. J Anim Sci Biotechnol 14:127, 2023. Pubmed reference: 37779189. DOI: 10.1186/s40104-023-00923-3.

2022

Davenport, K.M., Bickhart, D.M., Worley, K., Murali, S.C., Salavati, M., Clark, E.L., Cockett, N.E., Heaton, M.P., Smith, T.P.L., Murdoch, B.M., Rosen, B.D. :

An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. Gigascience 11:giab096, 2022. Pubmed reference: 35134925. DOI: 10.1093/gigascience/giab096.

Lv, F.H., Cao, Y.H., Liu, G.J., Luo, L.Y., Lu, R., Liu, M.J., Li, W.R., Zhou, P., Wang, X.H., Shen, M., Gao, L., Yang, J.Q., Yang, H., Yang, Y.L., Liu, C.B., Wan, P.C., Zhang, Y.S., Pi, W.H., Ren, Y.L., Shen, Z.Q., Wang, F., Wang, Y.T., Li, J.Q., Salehian-Dehkordi, H., Hehua, E., Liu, Y.G., Chen, J.F., Wang, J.K., Deng, X.M., Esmailizadeh, A., Dehghani-Qanatqestani, M., Charati, H., Nosrati, M., Štěpánek, O., Rushdi, H.E., Olsaker, I., Curik, I., Gorkhali, N.A., Paiva, S.R., Caetano, A.R., Ciani, E., Amills, M., Weimann, C., Erhardt, G., Amane, A., Mwacharo, J.M., Han, J.L., Hanotte, O., Periasamy, K., Johansson, A.M., Hallsson, J.H., Kantanen, J., Coltman, D.W., Bruford, M.W., Lenstra, J.A., Li, M.H. :

Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression, and agronomically important loci. Mol Biol Evol 39:msab353, 2022. Pubmed reference: 34893856. DOI: 10.1093/molbev/msab353.

Qiao, G., Xu, P., Guo, T., Wu, Y., Lu, X., Zhang, Q., He, X., Zhu, S., Zhao, H., Lei, Z., Sun, W., Yang, B., Yue, Y. :

Genetic basis of Dorper sheep (Ovis aries) revealed by long-Read de novo genome assembly. Front Genet 13:846449, 2022. Pubmed reference: 35480318. DOI: 10.3389/fgene.2022.846449.

2021

Salehian-Dehkordi, H., Xu, Y.X., Xu, S.S., Li, X., Luo, L.Y., Liu, Y.J., Wang, D.F., Cao, Y.H., Shen, M., Gao, L., Chen, Z.H., Glessner, J.T., Lenstra, J.A., Esmailizadeh, A., Li, M.H., Lv, F.H. :

Genome-wide detection of copy number variations and their association with distinct phenotypes in the world's sheep. Front Genet 12:670582, 2021. Pubmed reference: 34093663. DOI: 10.3389/fgene.2021.670582.

Wang, Z.H., Zhu, Q.H., Li, X., Zhu, J.W., Tian, D.M., Zhang, S.S., Kang, H.L., Li, C.P., Dong, L.L., Zhao, W.M., Li, M.H. :

iSheep: an integrated resource for sheep genome, variant and phenotype. Front Genet 12:714852, 2021. Pubmed reference: 34490043. DOI: 10.3389/fgene.2021.714852.

2020

Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T.P.L., Worley, K.C., Cockett, N.E., Archibald, A.L., Clarke, S.M., Murdoch, B.M., Clark, E.L. :

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0). Front Genet 11:580580, 2020. Pubmed reference: 33193703. DOI: 10.3389/fgene.2020.580580.

2014

Jiang, Y., Xie, M., Chen, W., Talbot, R., Maddox, J.F., Faraut, T., Wu, C., Muzny, D.M., Li, Y., Zhang, W., Stanton, J.A., Brauning, R., Barris, W.C., Hourlier, T., Aken, B.L., Searle, S.M.J., Adelson, D.L., Bian, C., Cam, G.R., Chen, Y., Cheng, S., DeSilva, U., Dixen, K., Dong, Y., Fan, G., Franklin, I.R., Fu, S., Guan, R., Highland, M.A., Holder, M.E., Huang, G., Ingham, A.B., Jhangiani, S.N., Kalra, D., Kovar, C.L., Lee, S.L., Liu, W., Liu, X., Lu, C., Lv, T., Mathew, T., McWilliam, S., Menzies, M., Pan, S., Robelin, D., Servin, B., Townley, D., Wang, W., Wei, B., White, S.N., Yang, X., Ye, C., Yue, Y., Zeng, P., Zhou, Q., Hansen, J.B., Kristensen, K., Gibbs, R.A., Flicek, P., Warkup, C.C., Jones, H.E., Oddy, V.H., Nicholas, F.W., McEwan, J.C., Kijas, J., Wang, J., Worley, K.C., Archibald, A.L., Cockett, N., Xu, X., Wang, W., Dalrymple, B.P. :

The sheep genome illuminates biology of the rumen and lipid metabolism. Science 344:1168-1173, 2014. Pubmed reference: 24904168. DOI: 10.1126/science.1252806.

2010

International Sheep Genomics Consortium, Archibald, A.L., Cockett, N.E., Dalrymple, B.P., Faraut, T., Kijas, J.W., Maddox, J.F., McEwan, J.C., Oddy, V.H., Raadsma, H.W., Wade, C., Wang, J., Wang, W., Xun, X. :

The sheep genome reference sequence: a work in progress. Anim Genet 41:449-53, 2010. Pubmed reference: 20809919. DOI: 10.1111/j.1365-2052.2010.02100.x.

2007

Dalrymple, B.P., Kirkness, E.F., Nefedov, M., McWilliam, S., Ratnakumar, A., Barris, W., Zhao, S., Shetty, J., Maddox, J.F., O'Grady, M., Nicholas, F., Crawford, A.M., Smith, T., de Jong, P.J., McEwan, J., Oddy, V.H., Cockett, N.E. :

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol 8:R152, 2007. Pubmed reference: 17663790. DOI: 10.1186/gb-2007-8-7-r152.

2006

Beraldi, D., McRae, AF., Gratten, J., Slate, J., Visscher, PM., Pemberton, JM. :

Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics 173:1521-37, 2006. Pubmed reference: 16868121. DOI: 10.1534/genetics.106.057141.

Cockett, N.E. :

The sheep genome. Genome Dyn 2:79-85, 2006. Pubmed reference: 18753771. DOI: 10.1159/000095096.

2001

Maddox, J.F., Davies, K.P., Crawford, A.M., Hulme, D.J., Vaiman, D., Cribiu, E.P., Freking, B.A., Beh, K.J., Cockett, N.E., Kang, N., Riffkin, C.D., Drinkwater, R., Moore, S.S., Dodds, K.G., Lumsden, J.M., van Stijn, T.C., Phua, S.H., Adelson, D.L., Burkin, H.R., Broom, J.E., Buitkamp, J., Cambridge, L., Cushwa, W.T., Gerard, E., Galloway, S.M., Harrison, B., Hawken, R.J., Hiendleder, S., Henry, H.M., Medrano, J.F., Paterson, K.A., Schibler, L., Stone, R.T., van Hest, B. :

An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 11:1275-89, 2001. Pubmed reference: 11435411. DOI: 10.1101/gr.135001.

1998

De Gortari, M.J., Freking, B.A., Cuthbertson, R.P., Kappes, S.M., Keele, J.W., Stone, R.T., Leymaster, K.A., Dodds, K.G., Crawford, A.M., Beattie, C.W. :

A second-generation linkage map of the sheep genome Mammalian Genome 9:204-209, 1998. Pubmed reference: 9501303.

1997

Yadav, B.R., Katiyar, P.K., Chauhan, M.S., Madan, M.L. :

Chromosome configuration during in vitro maturation of goat, sheep and buffalo oocytes. Theriogenology 47:943-51, 1997. Pubmed reference: 16728044. DOI: 10.1016/s0093-691x(97)00050-2.

1996

Galloway, S.M., Hanrahan, V., Dodds, K.G., Potts, M.D., Crawford, A.M., Hill, D.F. :

A linkage map of the ovine x chromosome Genome Research 6:667-677, 1996. Pubmed reference: 8858342.

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

Ansari, H.A., Maher, D.W., Pearce, P.D., Broad, T.E. :

Resolving ambiguities in the karyotype of domestic sheep (Ovis aries). II. G-, Q-, and R-banded idiograms, and chromosome-specific molecular markers. Chromosoma 105:62-7, 1996. Pubmed reference: 8662260. DOI: 10.1007/BF02510040.

Bhatia, S., Shanker, V. :

Chromosomes of Magra sheep. Indian Journal of Animal Sciences 66:511-515, 1996.

1995

Crawford, A.M., Dodds, K.G., Ede, A.J., Pierson, C.A., Montgomery, G.W., Garmonsway, H.G., Beattie, A.E., Davies, K., Maddox, J.F., Kappes, S.W., Stone, R.T., Nguyen, T.C., Penty, J.M., Lord, E.A., Broom, J.E., Buitkamp, J., Schwaiger, W., Epplen, J.T., Matthew, P., Matthews, M.E., Hulme, D.J., Beh, K.J., McGraw, R.A., Beattie, C.W. :

An autosomal genetic linkage map of the sheep genome Genetics 140:703-724, 1995. Pubmed reference: 7498748.

Iannuzzi, L., Di Meo, G.P. :

Iannuzzi, L., Di Meo, G.P., Perucatti, A., Ferrara, L. :

G- and R-banding comparison of sheep (Ovis aries L.) chromosomes. Cytogenet Cell Genet 68:85-90, 1995. Pubmed reference: 7956369. DOI: 10.1159/000133897.

Gupta, N., Gupta, S.C. :

The karyotype of Malpura sheep. Indian Journal of Animal Sciences 65:101-103, 1995.

1994

Echard, G., Broad, T.E., Hill, D., Pearce, P. :

Present Status of the Ovine Gene Map (Ovis aries) - Comparison with the Bovine Map (Bos taurus) Mammalian Genome 5:324-332, 1994. Pubmed reference: 8043945.

Crawford, A.M., Montgomery, G.W., Pierson, C.A., Brown, T., Dodds, K.G., Sunden, S.L.F., Henry, H.M., Ede, A.J., Swarbrick, P.A., Berryman, T., Penty, J.M., Hill, D.F. :

Sheep linkage mapping: Nineteen linkage groups derived from the analysis of paternal half-sib families Genetics 137:573-579, 1994. Pubmed reference: 8070667.

Broad, T.E., Hill, D.F. :

Mapping the Sheep Genome - Practice, Progress and Promise British Veterinary Journal 150:237-252, 1994. Pubmed reference: 7913869. DOI: 10.1016/S0007-1935(05)80004-1.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

Kaftanovskaya, H.M., Serov, O.L. :

High-resolution GTG-banded chromosomes of cattle, sheep, and goat: a comparative study. J Hered 85:395-400, 1994. Pubmed reference: 7963454. DOI: 10.1093/oxfordjournals.jhered.a111485.

Ansari, H.A., Bosma, A.A., Bunch, T.D., Long, S.E., Popescu, C.P. :

Clarification of chromosome nomenclature in the sheep (Ovis aries). Report of the committee for the standardization of the sheep karyotype. Cytogenet Cell Genet 67:114-5, 1994. Pubmed reference: 8039420. DOI: 10.1159/000133809.

Bhatia, S., Shanker, V. :

Cytogenetic Characteristics of Munjal Sheep. Indian Journal of Animal Sciences 64:975-977, 1994.

1993

Rajcan-Separovic, E., Sabour, M.P. :

Fluorescence in situ hybridization of bovine Alu-like sequences to bovine and ovine chromosomes. Genome 36:984-6, 1993. Pubmed reference: 8270208. DOI: 10.1139/g93-129.

Ansari, H.A., Pearce, P.D., Maher, D.W., Malcolm, A.A., Broad, T.E. :

Resolving ambiguities in the karyotype of domestic sheep (Ovis aries). Chromosoma 102:340-7, 1993. Pubmed reference: 8325165. DOI: 10.1007/BF00661277.

1992

Kaftanovskaya, H.M., Serov, O.L. :

High-Resolution G-Banding of Sheep Chromosomes. Journal of Heredity 83:92-99, 1992.

1991

Hediger, R., Ansari, H.A., Stranzinger, G.F. :

Hayes, H., Petit, E., Dutrillaux, B. :

Comparison of RBG-banded karyotypes of cattle, sheep, and goats. Cytogenet Cell Genet 57:51-5, 1991. Pubmed reference: 1855392. DOI: 10.1159/000133114.

Hayes, H., Petit, E. :

Comparison of RBG-Banded Karyotypes of Cattle, Sheep and Goat. Genetics Selection Evolution 23:S144-S147, 1991.

Bhatia, S., Shanker, V. :

C-Banding of the Chromosomes of Nali Sheep. Indian Journal of Animal Sciences 61:1238-1241, 1991.

1990

DiBerardina, D., Hayes, H., Fries, R., Long, S. :

Tateno, H., Akaike, M., Fukui, Y., Kamiguchi, Y., Mikamo, K. :

A method for chromosome analysis of ram spermatozoa using zona-free hamster oocytes. Theriogenology 34:845-52, 1990. Pubmed reference: 16726887. DOI: 10.1016/0093-691x(90)90556-9.

Bunch, T.D., Mitchell, R.M., Maciulis, A. :

G-Banded Chromosomes of the Gansu Argali (Ovis-Ammon-Jubata) and Their Implications in the Evolution of the Ovis Karyotype. Journal of Heredity 81:227-230, 1990.

1989

Mensher, S.H., Bunch, T.D., Maciulis, A. :

High-resolution G-banded karyotype and idiogram of the goat: a sheep-goat G-banded comparison. J Hered 80:150-5, 1989. Pubmed reference: 2926117. DOI: 10.1093/oxfordjournals.jhered.a110816.

Bhatia, S., Sharker, V. :

Chromosomes of Nali sheep. Indian Journal of Animal Sciences 59:297-299, 1989.

Di Berardino, D., Lioi, M.B., Miranda, C., Milia, A. di., D'Agostino, M.G., Matassino, D. :

R-banding pattern of the prometaphase chromosomes of the domestic sheep Ovis aries L. Genetique, Selection, Evolution 21:1-10, 1989.

1988

Matejka, M., Cribiu, E.P., Popescu, C.P. :

Diagrammatic representation of RBA-banded karyotype of domestic sheep (Ovis aries). J Hered 79:71-4, 1988. Pubmed reference: 3367042. DOI: 10.1093/oxfordjournals.jhered.a110454.

Long, S.E. :

Normal karyotype and karyotypic variants in sheep. Proceedings of the COGNOSAG Workshop 1986 :69-73, 1988.

Matejka, M., Cribiu, E.P. :

Basis for a standardized karyotype nomenclature in the sheep. Proceedings of the COGNOSAG Workshop 1986 :63-67, 1988.

Rcheulishvili, M.D., Dzhozhadze, T.A. :

[Cytogenetic characteristics of some breeds of domestic sheep]. Mater. nauch. issled. lab. biol. osnov. povysh. produktiv. zhivotnovod. In-ta Zool. AN GSSR. Tbilisi, USSR :235-242, 1988.

1987

Grafodatskiĭ, A.S., Biltueva, L.S. :

[Homology of G-banded mammalian chromosomes]. Genetika 23:93-103, 1987. Pubmed reference: 3469125.

Matejka, M., Cribiu, E. :

[Not Available]. Genet Sel Evol (1983) 19:113-26, 1987. Pubmed reference: 22879275. DOI: 10.1186/1297-9686-19-1-113.

1986

Chevelev, S.F. :

[Chromosomes of domestic sheep]. Veterinariya, Moscow :27-29, 1986.

1985

Swartz, H.A., Vogt, D.W., Michalski, K.A., Warren, J.E., Kiesling, D. :

Chromosomal evaluation of a ewe lamb with atresia ani vaginalis American Journal of Veterinary Research 46:2145-2146, 1985. Pubmed reference: 4062021.

Long, S.E. :

Standard nomenclature for the G-band karyotype of the domestic sheep (Ovis aries). Committee for standardized karyotype of Ovis aries. Hereditas 103:165-70, 1985. Pubmed reference: 4086317. DOI: 10.1111/j.1601-5223.1985.tb00497.x.

Solimeme, R., Franciscis, G. :

[Ethidium bromide for high- resolution chromosome banding of peripheral blood lymphocytes from sheep: first results]. Atti della Societa Italiana delle Scienze Veterinairie 39:413-415, 1985.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1973

Hansen, K.M. :

The karyotype of the domestic sheep (Ovis aries) identified by quinacrine mustard staining and fluorescence microscopy. Hereditas 75:233-40, 1973. Pubmed reference: 4131323. DOI: 10.1111/j.1601-5223.1973.tb01164.x.

1964

BORLAND, R. :

THE CHROMOSOMES OF DOMESTIC SHEEP. J Hered 55:61-4, 1964. Pubmed reference: 14154500. DOI: 10.1093/oxfordjournals.jhered.a107292.

1931

Wassin, B. :

Linkage studies in sheep Journal of Heredity 22:9-13, 1931.

None

[No authors listed] :

Sci Data 12:1351, None. Pubmed reference: 40760128. DOI: 10.1038/s41597-025-05650-0.

Ovis canadensis (bighorn sheep) :

2024

Deakin, S., Coltman, D.W. :

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis). PeerJ 12:e16946, 2024. Pubmed reference: 38426129. DOI: 10.7717/peerj.16946.

Ovis orientalis (Asiatic mouflon) :

2022

2020

Su, R., Qiao, X., Gao, Y., Li, X., Jiang, W., Chen, W., Fan, Y., Zheng, B., Zhang, Y., Liu, Z., Wang, R., Wang, Z., Wang, Z., Wan, W., Dong, Y., Li, J. :

Draft genome of the European mouflon (Ovis orientalis musimon). Front Genet 11:533611, 2020. Pubmed reference: 33329689. DOI: 10.3389/fgene.2020.533611.

Oxyeleotris marmorata (marble goby) :

2025

Liu, H., Yao, J., Dong, M., Yi, M., Liu, W. :

Chromosome-level genome assembly of the marble goby (Oxyeleotris marmorata). Sci Data 12:1596, 2025. Pubmed reference: 41028726. DOI: 10.1038/s41597-025-05878-w.

Ozotoceros bezoarticus (pampas deer) :

1995

Duarte, J.M.B., Giannoni, M.L. :

Cytogenetic analysis of the pampas deer, Ozotoceros bezoarticus (mammalia, cervidae). Revista Brasileira de Genetica 18:485-488, 1995.

Pagetodes antarcticus (long-fingered icefish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Pagetopsis macropterus :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Pagrus auratus (squirefish) :

2024

Blommaert, J., Sandoval-Castillo, J., Beheregaray, L., Wellenreuther, M. :

Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 116:110929, 2024. Pubmed reference: 39216708. DOI: 10.1016/j.ygeno.2024.110929.

Paleosuchus palpebrosus (Cuvier's dwarf caiman) :

2025

Colston, T.J., Pirro, S., Pyron, R.A. :

The complete genome sequences of 101 species of reptiles. Biodivers Genomes 2025, 2025. Pubmed reference: 40265171. DOI: 10.56179/001c.129597.

Pampus argenteus (silver pomfret) :

2024

Hu, J., Zhang, Y., Li, Y., Li, Y., Zhang, M., Huang, W., Xu, S., Wang, D., Wang, X., Liu, J., Wang, Y., Yan, X. :

Two high quality chromosome-scale genome assemblies of female and male silver pomfret (Pampus argenteus). Sci Data 11:1100, 2024. Pubmed reference: 39379396. DOI: 10.1038/s41597-024-03914-9.

Pan (chimpanzees) :

2025

Han, S., Riyahi, S., Huang, X., Kuhlwilm, M. :

A curated dataset of great ape genome diversity. Sci Data 12:1835, 2025. Pubmed reference: 41261097. DOI: 10.1038/s41597-025-06124-z.

Pan paniscus (pygmy chimpanzee) :

2025

Han, S., Riyahi, S., Huang, X., Kuhlwilm, M. :

A curated dataset of great ape genome diversity. Sci Data 12:1835, 2025. Pubmed reference: 41261097. DOI: 10.1038/s41597-025-06124-z.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Pan troglodytes (chimpanzee) :

2025

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Pangasianodon hypophthalmus (striped catfish) :

2025

Zhang, X., Huang, Y., Zhou, W., Chen, J., Zhu, Z., Xu, Y., Wang, X., Xu, J., Shi, Q. :

A telomere-to-telomere gap-free genome assembly of the striped catfish (Pangasianodon hypophthalmus). Sci Data 12:1890, 2025. Pubmed reference: 41315526. DOI: 10.1038/s41597-025-06161-8.

2021

Gao, Z., You, X., Zhang, X., Chen, J., Xu, T., Huang, Y., Lin, X., Xu, J., Bian, C., Shi, Q. :

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus). Genomics 113:3349-3356, 2021. Pubmed reference: 34343676. DOI: 10.1016/j.ygeno.2021.07.026.

Panthera onca (jaguar) :

2025

Zenato Lazzari, G., Figueiró, H.V., Sartor, C.C., Donadio, E., Di Martino, S., Draheim, H.M., Eizirik, E. :

Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca). Ecol Evol 15:e71465, 2025. Pubmed reference: 40416754. DOI: 10.1002/ece3.71465.

[No authors listed] :

Correction to "Development of a SNP panel for geographic assignment and population monitoring of jaguars (Panthera onca)". Ecol Evol 15:e71764, 2025. Pubmed reference: 40630084. DOI: 10.1002/ece3.71764.

Panthera pardus (leopard) :

2024

Li, H.M., Liu, B.Y., Shi, M.H., Zhang, L., Yang, S.C., Sahu, S.K., Cui, L.Y., Liu, S.L., Dussex, N., Ma, Y., Liu, D., Kong, W.Y., Lu, H.R., Zhao, Y., Dalén, L., Liu, H., Lan, T.M., Jiang, G.S., Xu, Y.C. :

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard. Zool Res 45:2095-8137(2024)03-0464-04:464-467, 2024. Pubmed reference: 38583937. DOI: 10.24272/j.issn.2095-8137.2023.232.

2023

Mochales-Riaño, G., Fontsere, C., de Manuel, M., Talavera, A., Burriel-Carranza, B., Tejero-Cicuéndez, H., AlGethami, R.H.M., Shobrak, M., Marques-Bonet, T., Carranza, S. :

Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr). iScience 26:107481, 2023. Pubmed reference: 37601769. DOI: 10.1016/j.isci.2023.107481.

Panthera tigris (tiger) :

2024

Das, A., Suvo, M.S.H., Shaha, M., Gupta, M.D. :

Genome sequencing of captive white tigers from Bangladesh. BMC Genom Data 25:52, 2024. Pubmed reference: 38844863. DOI: 10.1186/s12863-024-01239-5.

Lan, T., Li, H., Liu, B., Shi, M., Tian, Y., Sahu, S.K., Cui, L., Dussex, N., Liu, D., Ma, Y., Kong, W., Liu, S., Fan, J., Zhao, Y., Fu, Y., Li, Q., Lin, C., Dalén, L., Liu, H., Zhang, L., Jiang, G., Xu, Y. :

Revealing extensive inbreeding and less-efficient purging of deleterious mutations in wild Amur tigers in China. J Genet Genomics 52:641-649, 2024. Pubmed reference: 39674273. DOI: 10.1016/j.jgg.2024.12.004.

2013

Cho, Y.S., Hu, L., Hou, H., Lee, H., Xu, J., Kwon, S., Oh, S., Kim, H.M., Jho, S., Kim, S., Shin, Y.A., Kim, B.C., Kim, H., Kim, C.U., Luo, S.J., Johnson, W.E., Koepfli, K.P., Schmidt-Küntzel, A., Turner, J.A., Marker, L., Harper, C., Miller, S.M., Jacobs, W., Bertola, L.D., Kim, T.H., Lee, S., Zhou, Q., Jung, H.J., Xu, X., Gadhvi, P., Xu, P., Xiong, Y., Luo, Y., Pan, S., Gou, C., Chu, X., Zhang, J., Liu, S., He, J., Chen, Y., Yang, L., Yang, Y., He, J., Liu, S., Wang, J., Kim, C.H., Kwak, H., Kim, J.S., Hwang, S., Ko, J., Kim, C.B., Kim, S., Bayarlkhagva, D., Paek, W.K., Kim, S.J., O'Brien, S.J., Wang, J., Bhak, J. :

The tiger genome and comparative analysis with lion and snow leopard genomes. Nat Commun 4:2433, 2013. Pubmed reference: 24045858. DOI: 10.1038/ncomms3433.

Panthera uncia (snow leopard) :

2025

Yang, L., Jin, H., Yang, Q., Poyarkov, A., Korablev, M., Rozhnov, V., Shao, J., Fu, Q., Hernandez-Blanco, J.A., Zhan, X., Yu, L., Alexandrov, D., Dai, Q., Munkhtsog, B., Du, X., Munkhtsog, B., Ma, L., Chen, W., Malykh, S., Jin, Y., He, S., Zhang, T., Wu, G., Shi, Y., Wei, F., Hu, Y. :

Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards. Genome Biol 26:94, 2025. Pubmed reference: 40229771. DOI: 10.1186/s13059-025-03555-0.

Martin, P., Sven, W., Karla, S., Leona, V., April, J., Jan, F., Pamela, B.A., Petr, H. :

A chromosome-level genome assembly of the snow leopard, Panthera uncia. J Hered :esaf046, 2025. Pubmed reference: 40632105. DOI: 10.1093/jhered/esaf046.

Pantherophis alleghaniensis :

2023

Burbrink, F.T., Harrington, S.M., Bobo, D., Myers, E.A. :

Considering admixture when producing draft genomes: an example in North American ratsnakes (P. alleghaniensis/P. obsoletus). G3 (Bethesda) 13:jkad113, 2023. Pubmed reference: 37228097. DOI: 10.1093/g3journal/jkad113.

Pantherophis guttatus (corn snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

2020

Ullate-Agote, A., Burgelin, I., Debry, A., Langrez, C., Montange, F., Peraldi, R., Daraspe, J., Kaessmann, H., Milinkovitch, M.C., Tzika, A.C. :

Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. Proc Natl Acad Sci U S A 117:26307-26317, 2020. Pubmed reference: 33020272. DOI: 10.1073/pnas.2003724117.

2014

Ullate-Agote, A., Milinkovitch, M.C., Tzika, A.C. :

The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates. Int J Dev Biol 58:881-8, 2014. Pubmed reference: 26154328. DOI: 10.1387/ijdb.150060at.

Pantholops hodgsonii (chiru) :

2024

Xu, B., Chen, J., Song, P., Gu, H., Jiang, F., Li, B., Wei, Q., Zhang, T. :

A high-quality chromosome-level reference genome assembly of Tibetan antelope (Pantholops hodgsonii). Sci Data 11:1215, 2024. Pubmed reference: 39532915. DOI: 10.1038/s41597-024-04089-z.

Papio (baboons) :

2023

Sørensen, E.F., Harris, R.A., Zhang, L., Raveendran, M., Kuderna, L.F.K., Walker, J.A., Storer, J.M., Kuhlwilm, M., Fontsere, C., Seshadri, L., Bergey, C.M., Burrell, A.S., Bergman, J., Phillips-Conroy, J.E., Shiferaw, F., Chiou, K.L., Chuma, I.S., Keyyu, J.D., Fischer, J., Gingras, M.C., Salvi, S., Doddapaneni, H., Schierup, M.H., Batzer, M.A., Jolly, C.J., Knauf, S., Zinner, D., Farh, K.K., Marques-Bonet, T., Munch, K., Roos, C., Rogers, J. :

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 380:eabn8153, 2023. Pubmed reference: 37262153. DOI: 10.1126/science.abn8153.

Parabramis pekinensis (white Amur bream) :

2025

Gu, H., Zhang, X., Xu, W., Yang, Z., Xu, Y., Miao, X., Feng, Y. :

Chromosome-level assemblies of the White bream Parabramis pekinensis. Sci Data 12:871, 2025. Pubmed reference: 40425610. DOI: 10.1038/s41597-025-04821-3.

Paracanthobrama guichenoti :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Paralichthys olivaceus (Japanese flounder) :

2024

Kim, J., Kim, Y., Shin, J., Kim, Y.K., Lee, D.H., Park, J.W., Lee, D., Kim, H.C., Lee, J.H., Lee, S.H., Kim, J. :

Fully phased genome assemblies and graph-based genetic variants of the olive flounder, Paralichthys olivaceus. Sci Data 11:1193, 2024. Pubmed reference: 39496665. DOI: 10.1038/s41597-024-04033-1.

Kim, J., Kim, Y., Shin, J., Kim, Y.K., Lee, D.H., Park, J.W., Lee, D., Kim, H.C., Lee, J.H., Lee, S.H., Kim, J. :

Author Correction: Fully phased genome assemblies and graph-based genetic variants of the olive flounder, Paralichthys olivaceus. Sci Data 11:1415, 2024. Pubmed reference: 39706846. DOI: 10.1038/s41597-024-04273-1.

Paralichthys orbignyanus :

2024

Villarreal, F., Burguener, G.F., Sosa, E.J., Stocchi, N., Somoza, G.M., Turjanski, A.G., Blanco, A., Viñas, J., Mechaly, A.S. :

Genome sequencing and analysis of black flounder (Paralichthys orbignyanus) reveals new insights into Pleuronectiformes genomic size and structure. BMC Genomics 25:297, 2024. Pubmed reference: 38509481. DOI: 10.1186/s12864-024-10081-z.

Paramisgurnus dabryanus :

2025

Zhang, L., Zhang, W., Cheng, Y., Fang, Y., Guan, X., Gong, A., Jiang, Y., Duan, Y., Huang, L., Younas, W., Wang, Y., Shi, M., Xia, X.Q. :

Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus). Sci Data 12:155, 2025. Pubmed reference: 39865085. DOI: 10.1038/s41597-025-04498-8.

Parapercis pulchella (harlequin sandsmelt) :

2024

Yao, A., Kohtsuka, H., Miura, T. :

Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella). Mar Genomics 73:S1874-7787(24)00004-7:101086, 2024. Pubmed reference: 38365348. DOI: 10.1016/j.margen.2024.101086.

Parupeneus biaculeatus :

2025

Luo, Z., Yi, M., Yang, X., Luo, Z., Li, X., Jiang, C., Kang, B., Huang, L., Lin, H.D., He, X., Yan, Y. :

The first high-quality chromosome-level genome of Parupeneus biaculeatus using HiFi and Hi-C data. Sci Data 12:1042, 2025. Pubmed reference: 40541970. DOI: 10.1038/s41597-025-05226-y.

Parus major (Great Tit) :

2024

Spurgin, L.G., Bosse, M., Adriaensen, F., Albayrak, T., Barboutis, C., Belda, E., Bushuev, A., Cecere, J.G., Charmantier, A., Cichon, M., Dingemanse, N.J., Doligez, B., Eeva, T., Erikstad, K.E., Fedorov, V., Griggio, M., Heylen, D., Hille, S., Hinde, C.A., Ivankina, E., Kempenaers, B., Kerimov, A., Krist, M., Kvist, L., Laine, V.N., Mänd, R., Matthysen, E., Nager, R., Nikolov, B.P., Norte, A.C., Orell, M., Ouyang, J., Petrova-Dinkova, G., Richner, H., Rubolini, D., Slagsvold, T., Tilgar, V., Török, J., Tschirren, B., Vágási, C.I., Yuta, T., Groenen, M.A.M., Visser, M.E., van Oers, K., Sheldon, B.C., Slate, J. :

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 24:e13969, 2024. Pubmed reference: 38747336. DOI: 10.1111/1755-0998.13969.

Passer domesticus (House sparrow) :

2025

Kumar, V., Sharma, G., Sharma, S., Prasad, S., Desai, S., Vaishnani, T., Vishnudasan, D., Maheswaran, G., Tyagi, K., Tyagi, I., Kavi Kishor, P.B., Chaubey, G., Suravajhala, P. :

Whole genome sequencing and assembly of the house sparrow, Passer domesticus. GigaByte 2025:gigabyte161, 2025. Pubmed reference: 40740214. DOI: 10.46471/gigabyte.161.

2023

Magallanes-Alba, M.E., Baricalla, A., Rego, N., Brun, A., Karasov, W.H., Caviedes-Vidal, E. :

Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation. Biol Methods Protoc 8:bpad013, 2023. Pubmed reference: 37521110. DOI: 10.1093/biomethods/bpad013.

Passer montanus (Eurasian tree sparrow) :

2023

Wang, S., Shen, Y., Lin, Z., Miao, Y., Wang, C., Zhang, W., Zhang, Y. :

New genes driven by segmental duplications share a testis-specific expression pattern in the chromosome-level genome assembly of tree sparrow. Integr Zool 19:1004-1008, 2023. Pubmed reference: 38014459. DOI: 10.1111/1749-4877.12789.

Passerculus sandwichensis (Savannah sparrow) :

2024

Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W., Bowie, R.C.K. :

Pavo cristatus (Indian peafowl) :

2025

Wang, G., Zhang, X., Zhao, X., Ren, X., Chen, A., Dai, W., Zhang, L., Lu, Y., Jiang, Z., Wang, H., Liu, Y., Zhao, X., Wen, J., Cheng, X., Zhang, Y., Ning, Z., Ban, L., Qu, L. :

Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of leucistic plumage of blue peafowl. Gigascience 14:giae124, 2025. Pubmed reference: 39965774. DOI: 10.1093/gigascience/giae124.

2023

Chakraborty, A., Mondal, S., Mahajan, S., Sharma, V.K. :

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl. Heliyon 9:e18571, 2023. Pubmed reference: 37576271. DOI: 10.1016/j.heliyon.2023.e18571.

Pelochelys cantorii (Cantor's giant softshell turtle) :

2023

Hong, X., Liu, H., Wang, Y., Li, M., Ji, L., Wang, K., Wei, C., Li, W., Chen, C., Yu, L., Zhu, X., Liu, X. :

A chromosome-level genome assembly of the Asian giant softshell turtle Pelochelys cantorii. Sci Data 10:754, 2023. Pubmed reference: 37914689. DOI: 10.1038/s41597-023-02667-1.

Pelodiscus sinensis (Chinese soft-shelled turtle) :

2025

Chen, J., Yao, J., Yuan, X., Huang, L., Peng, X., Bu, X., Jiao, J., Zhang, H. :

Chromosome-level genome assembly of the Chinese soft-shelled turtle Pelodiscus sinensis. Sci Data 12:1575, 2025. Pubmed reference: 41022891. DOI: 10.1038/s41597-025-05806-y.

Penaeus monodon (black tiger shrimp) :

2018

Huerlimann, R., Wade, N.M., Gordon, L., Montenegro, J.D., Goodall, J., McWilliam, S., Tinning, M., Siemering, K., Giardina, E., Donovan, D., Sellars, M.J., Cowley, J.A., Condon, K., Coman, G.J., Khatkar, M.S., Raadsma, H.W., Maes, G.E., Zenger, K.R., Jerry, D.R. :

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Sci Rep 8:13553, 2018. Pubmed reference: 30202061. DOI: 10.1038/s41598-018-31148-4.

Pennahia pawak :

2025

Jiang, L., Zheng, P., Zheng, J., Liu, Y., Song, W., Chen, S., Jin, W., Yan, X. :

Chromosome-level genome assembly and annotation of pawak croaker (Pennahia pawak). Sci Data 12:412, 2025. Pubmed reference: 40064941. DOI: 10.1038/s41597-025-04745-y.

Percocypris pingi (parma pingova) :

2024

He, Z., Li, C., Gao, K., Zheng, X., Wang, X., Wang, H., Chen, Q., Tang, Z., Zhang, M., Yang, D., Yan, T. :

The whole chromosome-level genome provides resources and insights into the endangered fish Percocypris pingi evolution and conservation. BMC Genomics 25:1175, 2024. Pubmed reference: 39627733. DOI: 10.1186/s12864-024-11100-9.

Perdix hodgsoniae (Tibetan partridge) :

2023

Zhou, C., Zheng, X., Feng, K., Peng, K., Zhang, Y., Zhao, G., Meng, Y., Zhang, L., Yue, B., Wu, Y. :

The draft genome of the Tibetan partridge (Perdix hodgsoniae) provides insights into its phylogenetic position and high-altitude adaptation. J Hered 114:175-188, 2023. Pubmed reference: 36546409. DOI: 10.1093/jhered/esac069.

Periophthalmus magnuspinnatus :

2024

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Periophthalmus modestus (shuttles hoppfish) :

2024

Bian, C., Huang, Y., Li, R., Xu, P., You, X., Lv, Y., Ruan, Z., Chen, J., Xu, J., Shi, Q. :

Perisoreus infaustus :

2009

Jaari, S., Li, M.H., Merilä, J. :

A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution. BMC Genomics 10:1, 2009. Pubmed reference: 19121221. DOI: 10.1186/1471-2164-10-1.

Perognathus longimembris (little pocket mouse) :

2024

Kozak, K.M., Escalona, M., Chumchim, N., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., Seligmann, W., Conroy, C., Patton, J.L., Bowie, R.C.K., Nachman, M.W. :

A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris. J Hered 115:130-138, 2024. Pubmed reference: 37793045. DOI: 10.1093/jhered/esad060.

Peromyscus polionotus (oldfield mouse) :

2022

Wooldridge, T.B., Kautt, A.F., Lassance, J.M., McFadden, S., Domingues, V.S., Mallarino, R., Hoekstra, H.E. :

An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proc Natl Acad Sci U S A 119:e2202862119, 2022. Pubmed reference: 35776547. DOI: 10.1073/pnas.2202862119.

Petrogale (rock wallabies) :

1996

Close, R.L., Bell, J.N., Dollin, A.E., Harding, H.R. :

Spermatogenesis and synaptonemal complexes of hybrid Petrogale (Marsupialia). J Hered 87:96-107, 1996. Pubmed reference: 8830099. DOI: 10.1093/oxfordjournals.jhered.a022982.

1993

Eldridge, M.D., Johnston, P.G. :

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). VIII. An investigation of the nonrandom nature of karyotypic change. Genome 36:524-34, 1993. Pubmed reference: 8349127. DOI: 10.1139/g93-072.

1992

Eldridge, M.D., Johnston, P.G., Close, R.L. :

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). VI. Determination of the plesiomorphic karyotype: G-banding comparison of Thylogale with Petrogale persephone, P. xanthopus, and P. l. lateralis. Cytogenet Cell Genet 61:29-33, 1992. Pubmed reference: 1505228. DOI: 10.1159/000133364.

Eldridge, M.D., Johnston, P.G., Lowry, P.S. :

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). VII. G-banding analysis of Petrogale brachyotis and P. concinna: species with dramatically altered karyotypes. Cytogenet Cell Genet 61:34-9, 1992. Pubmed reference: 1505229. DOI: 10.1159/000133365.

1991

Eldridge, M.D.B., Close, R.L., Johnston, P.G. :

Chromosomal Rearrangements in Rock Wallabies, Petrogale (Marsupialia, Macropodidae) .4. G-Banding Analysis of the Petrogale-Lateralis Complex. Australian Journal of Zoology 39:621-627, 1991.

Eldridge, M.D.B., Johnston, P.G., Close, R.L. :

Chromosomal Rearrangements in Rock Wallabies, Petrogale (Marsupialia, Macropodidae) .5. Chromosomal Phylogeny of the Lateralis- Penicillata Group. Australian Journal of Zoology 39:629-641, 1991.

1990

Eldridge, M.D.B., Close, R.L., Johnston, P.G. :

Chromosomal Rearrangements in Rock Wallabies, Petrogale (Marsupialia, Macropodidae) .3. G-Banding Analysis of Petrogale-Inornata and P-Penicillata. Genome 33:798-802, 1990.

Sharman, G.B., Close, R.L., Maynes, G.M. :

Chromosome Evolution, Phylogeny and Speciation of Rock Wallabies (Petrogale, Macropodidae). Australian Journal of Zoology 37:351-363, 1990.

1989

Eldridge, M.D., Johnston, P.G., Close, R.L., Lowry, P.S. :

Chromosomal rearrangements in rock wallabies, Petrogale (Marsupialia: Macropodidae). II. G-banding analysis of Petrogale godmani. Genome 32:935-40, 1989. Pubmed reference: 2628158. DOI: 10.1139/g89-534.

Petromyzon marinus (sea lamprey) :

2023

Timoshevskaya, N., Eşkut, K.I., Timoshevskiy, V.A., Robb, S.M.C., Holt, C., Hess, J.E., Parker, H.J., Baker, C.F., Miller, A.K., Saraceno, C., Yandell, M., Krumlauf, R., Narum, S.R., Lampman, R.T., Gemmell, N.J., Mountcastle, J., Haase, B., Balacco, J.R., Formenti, G., Pelan, S., Sims, Y., Howe, K., Fedrigo, O., Jarvis, E.D., Smith, J.J. :

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. Cell Rep 42:112263, 2023. Pubmed reference: 36930644. DOI: 10.1016/j.celrep.2023.112263.

Phacochoerus africanus (Common warthog) :

2023

Feng, W., Zhou, L., Zhao, P., Du, H., Diao, C., Zhang, Y., Liu, Z., Jin, W., Yu, J., Han, J., Okoth, E., Mrode, R., Liu, J.F. :

Comparative genomic analysis of warthog and Sus scrofa identifies adaptive genes associated with African swine fever. Biology (Basel) 12:1001, 2023. Pubmed reference: 37508430. DOI: 10.3390/biology12071001.

Phascolarctos cinereus (koala) :

2024

Lott, M.J., Frankham, G.J., Eldridge, M.D.B., Alquezar-Planas, D.E., Donnelly, L., Zenger, K.R., Leigh, K.A., Kjeldsen, S.R., Field, M.A., Lemon, J., Lunney, D., Crowther, M.S., Krockenberger, M.B., Fisher, M., Neaves, L.E. :

Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes. Ecol Evol 14:e11700, 2024. Pubmed reference: 39091325. DOI: 10.1002/ece3.11700.

2023

Hogg, C.J., Silver, L., McLennan, E.A., Belov, K. :

Koala genome survey: An open data resource to improve conservation planning. Genes (Basel) 14:546, 2023. Pubmed reference: 36980819. DOI: 10.3390/genes14030546.

2018

Johnson, R.N., O'Meally, D., Chen, Z., Etherington, G.J., Ho, S.Y.W., Nash, W.J., Grueber, C.E., Cheng, Y., Whittington, C.M., Dennison, S., Peel, E., Haerty, W., O'Neill, R.J., Colgan, D., Russell, T.L., Alquezar-Planas, D.E., Attenbrow, V., Bragg, J.G., Brandies, P.A., Chong, A.Y., Deakin, J.E., Di Palma, F., Duda, Z., Eldridge, M.D.B., Ewart, K.M., Hogg, C.J., Frankham, G.J., Georges, A., Gillett, A.K., Govendir, M., Greenwood, A.D., Hayakawa, T., Helgen, K.M., Hobbs, M., Holleley, C.E., Heider, T.N., Jones, E.A., King, A., Madden, D., Graves, J.A.M., Morris, K.M., Neaves, L.E., Patel, H.R., Polkinghorne, A., Renfree, M.B., Robin, C., Salinas, R., Tsangaras, K., Waters, P.D., Waters, S.A., Wright, B., Wilkins, M.R., Timms, P., Belov, K. :

Adaptation and conservation insights from the koala genome. Nat Genet 50:1102-1111, 2018. Pubmed reference: 29967444. DOI: 10.1038/s41588-018-0153-5.

Philantomba maxwellii (Maxwell's duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Philantomba monticola (Blue duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Phocoena sinus (vaquita) :

2021

Morin, P.A., Archer, F.I., Avila, C.D., Balacco, J.R., Bukhman, Y.V., Chow, W., Fedrigo, O., Formenti, G., Fronczek, J.A., Fungtammasan, A., Gulland, F.M.D., Haase, B., Peter Heide-Jorgensen, M., Houck, M.L., Howe, K., Misuraca, A.C., Mountcastle, J., Musser, W., Paez, S., Pelan, S., Phillippy, A., Rhie, A., Robinson, J., Rojas-Bracho, L., Rowles, T.K., Ryder, O.A., Smith, C.R., Stevenson, S., Taylor, B.L., Teilmann, J., Torrance, J., Wells, R.S., Westgate, A.J., Jarvis, E.D. :

Reference genome and demographic history of the most endangered marine mammal, the vaquita. Mol Ecol Resour 21:1008-1020, 2021. Pubmed reference: 33089966. DOI: 10.1111/1755-0998.13284.

Phodilus badius (oriental bay-owl) :

2025

Hains, T., Catanach, T., Pirro, S., Bates, J., Hackett, S. :

The complete genome sequences of 22 species of owls (Strigiformes, Aves). Biodivers Genomes 2025, 2025. Pubmed reference: 39830368. DOI: 10.56179/001c.128167.

Phodopus roborovskii (desert hamster) :

2022

Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J., Wyler, E. :

De novo-whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome: An animal model for severe/critical COVID-19. Genome Biol Evol 14:evac100, 2022. Pubmed reference: 35778793. DOI: 10.1093/gbe/evac100.

Phoenicurus ochruros (black redstart) :

2025

Ghimire, P., Wang, N., Hu, Y., Lamichhaney, S. :

A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros). Sci Data 12:1885, 2025. Pubmed reference: 41315292. DOI: 10.1038/s41597-025-06156-5.

Phoxinus phoxinus (Eurasian minnow) :

2025

Oriowo, T.O., Chrysostomakis, I., Martin, S., Kukowka, S., Brown, T., Winkler, S., Myers, E.W., Böhne, A., Stange, M. :

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity. Gigascience 14:giae116, 2025. Pubmed reference: 39877992. DOI: 10.1093/gigascience/giae116.

Phrynocephalus forsythii :

2023

Qi, Y., Zhao, W., Zhao, Y., Niu, C., Cao, S., Zhang, Y. :

Chromosome-level genome assembly of Phrynocephalus forsythii using third-generation DNA sequencing and Hi-C analysis. DNA Res 30:dsad003, 2023. Pubmed reference: 36882113. DOI: 10.1093/dnares/dsad003.

Phrynosoma blainvillii :

2023

Richmond, J.Q., McGuire, J.A., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Fisher, R.N., Wang, I.J., Shaffer, H.B. :

Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii. J Hered 114:410-417, 2023. Pubmed reference: 37195437. DOI: 10.1093/jhered/esad032.

Phyllobates terribilis :

2025

Márquez, R., Jacob Machado, D., Nouri, R., Gendreau, K.L., Janies, D., Saporito, R.A., Kronforst, M.R., Grant, T. :

A draft genome assembly for the dart-poison frog Phyllobates terribilis. GigaByte 2025:gigabyte157, 2025. Pubmed reference: 40590045. DOI: 10.46471/gigabyte.157.

Phyllostomus discolor (pale spear-nosed bat) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Picus viridis (Eurasian green woodpecker) :

2024

Forest, T., Achaz, G., Marbouty, M., Bignaud, A., Thierry, A., Koszul, R., Milhes, M., Lledo, J., Pons, J.M., Fuchs, J. :

Chromosome-level genome assembly of the European green woodpecker Picus viridis. G3 (Bethesda) 14:jkae042, 2024. Pubmed reference: 38537260. DOI: 10.1093/g3journal/jkae042.

Pipistrellus hanaki (Hanaki's dwarf bat) :

2025

Georgakakis, P., Karakasi, D., Lymberakis, P., Papadimitrakis, M., Stratakis, M., Bitzilekis, E., Poulakakis, N., Böhne, A., Monteiro, R., Fernández, R., Escudero, N. :

ERGA-BGE reference genome of Hanak's bat (Pipistrellus hanaki), an IUCN Vulnerable species restricted to forest-like biotopes. Open Res Eur 5:298, 2025. Pubmed reference: 41280292. DOI: 10.12688/openreseurope.20937.2.

Pipistrellus nathusii (Nathusius's pipistrelle) :

2024

Driller, M., Brown, T., Currie, S.E., Hiller, M., Winkler, S., Pippel, M., Voigt, C.C., Fickel, J., Mazzoni, C.J. :

A Haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839). DNA Res 31:dsae018, 2024. Pubmed reference: 38847751. DOI: 10.1093/dnares/dsae018.

Pituophis catenifer (gopher snake) :

2025

Grismer, J.L., Escalona, M., Miller, C., Marimuthu, M.P.A., Nguyen, O., Beraut, E., Sacco, S., Toffelmier, E., Cooper, R., Wang, I.J., Fisher, R.N., Shaffer, H.B. :

Reference genome of the Gophersnake, Pituophis catenifer (Serpentes: Colubridae). J Hered 116:663-672, 2025. Pubmed reference: 40319346. DOI: 10.1093/jhered/esaf024.

Plagiognathops microlepis (smallscale yellowfin) :

2024

Wu, Y., Sha, H., Luo, X., Zou, G., Liang, H. :

Chromosome-level genome assembly of Plagiognathops microlepis based on PacBio HiFi and Hi-C sequencing. Sci Data 11:802, 2024. Pubmed reference: 39030192. DOI: 10.1038/s41597-024-03645-x.

Liang, Y., Liu, H., Lu, W., Li, J., Fang, T., Gao, N., Chen, C., Zhao, X., Yang, K., Liu, H. :

Chromosome-level genome assembly of the smallscale yellowfin (Plagiognathops microlepis). Sci Data 11:1234, 2024. Pubmed reference: 39548126. DOI: 10.1038/s41597-024-04105-2.

Platalea minor (black-faced spoonbill) :

2024

[No authors listed] :

Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor. GigaByte 2024:1-13, 2024. Pubmed reference: 39071178. DOI: 10.46471/gigabyte.130.

Platanista gangetica (Ganges River dolphin) :

2025

Sharma, S.P., Ghazi, M.G., Das, G.C., Usmani, A.A., Badola, R., Hussain, S.A. :

Genome assembly of Gangetic dolphin (Platanista gangetica) reveals signature of regressive evolution. Genome Biol Evol :evaf227, 2025. Pubmed reference: 41320830. DOI: 10.1093/gbe/evaf227.

Platanista minor (Indus River dolphin) :

2025

Ibrahim, A., Chai, S., Zhong, C., Jieqiong, K., Ali, A., Hussain, S., Ali, H., Hussain, T., Waqas, U., Yang, G. :

Low heterozygosity and historical bottleneck effect depicted from the genome assembly of the Indus river dolphin (Platanista minor). Ecol Evol 15:e71462, 2025. Pubmed reference: 40416769. DOI: 10.1002/ece3.71462.

Platichthys flesus (European flounder) :

2024

Pomianowski, K., Kulczykowska, E., Burzyński, A. :

Genome guided, organ-specific transcriptome assembly of the European flounder (P. flesus) from the Baltic Sea. Sci Data 11:1184, 2024. Pubmed reference: 39477936. DOI: 10.1038/s41597-024-04004-6.

Platycercus elegans (crimson rosella) :

2025

Lachenicht, C., Termignoni-Garcia, F., Berg, M.L., Edwards, S.V., Bennett, A.T.D. :

Draft genome of the Crimson rosella (Platycercus elegans elegans), an Australian parrot and key resource for the study of host-pathogen interaction in Psittaciformes. BMC Genom Data 26:90, 2025. Pubmed reference: 41331439. DOI: 10.1186/s12863-025-01373-8.

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Plecoglossus altivelis (ayu) :

2023

Nakamoto, M., Sakamoto, T. :

Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing. BMC Res Notes 16:92, 2023. Pubmed reference: 37254197. DOI: 10.1186/s13104-023-06362-7.

2021

Nakamoto, M., Uchino, T., Koshimizu, E., Kuchiishi, Y., Sekiguchi, R., Wang, L., Sudo, R., Endo, M., Guiguen, Y., Schartl, M., Postlethwait, J.H., Sakamoto, T. :

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis. PLoS Genet 17:e1009705, 2021. Pubmed reference: 34437539. DOI: 10.1371/journal.pgen.1009705.

Plectropomus leopardus (leopard coralgrouper) :

2023

Han, W., Wu, S., Ding, H., Wang, M., Wang, M., Bao, Z., Wang, B., Hu, J. :

Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper. Sci Data 10:156, 2023. Pubmed reference: 36949049. DOI: 10.1038/s41597-023-02051-z.

Plecturocebus cupreus (coppery titi) :

None

[No authors listed] :

Genome Biol Evol 16:evae108, None. Pubmed reference: 38758096. DOI: 10.1093/gbe/evae108.

Plestiodon gilberti :

2025

Richmond, J.Q., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Toffelmier, E., Karin, B.R., Cooper, R.D., Fisher, R.N., Wang, I.J., Shaffer, H.B. :

A chromosome-level reference genome assembly for Gilbert's skink Plestiodon gilberti. J Hered :esaf040, 2025. Pubmed reference: 40581366. DOI: 10.1093/jhered/esaf040.

Pleurodeles waltl (Iberian ribbed newt) :

2025

Yassouf, M.Y., Kinoshita, A., Hasan, M.M., Li, T.S. :

Improved transcriptome assembly and functional annotation of Pleurodeles waltl for regeneration research. PLoS One 20:e0323196, 2025. Pubmed reference: 40367087. DOI: 10.1371/journal.pone.0323196.

None

[No authors listed] :

iScience 28:113535, None. Pubmed reference: 41069852. DOI: 10.1016/j.isci.2025.113535.

Plotosus lineatus (striped eel catfish) :

2023

Shao, F., Wu, Z.C., Xu, Y., Li, P., Peng, Z.G. :

Genome of striped eel catfish (Plotosus lineatus) provides insights into the adaptive evolution of amphidromous fish. Zool Res 44:349-352, 2023. Pubmed reference: 36849790. DOI: 10.24272/j.issn.2095-8137.2022.387.

Podarcis lilfordi (Lilford's wall lizard) :

2023

Gomez-Garrido, J., Cruz, F., Alioto, T.S., Feiner, N., Uller, T., Gut, M., Sanchez Escudero, I., Tavecchia, G., Rotger, A., Otalora Acevedo, K.E., Baldo, L. :

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Res 30:dsad008, 2023. Pubmed reference: 37137526. DOI: 10.1093/dnares/dsad008.

Podarcis raffonei (Aeolian wall lizard) :

2023

Gabrielli, M., Benazzo, A., Biello, R., Ancona, L., Fuselli, S., Iannucci, A., Balacco, J., Mountcastle, J., Tracey, A., Ficetola, G.F., Salvi, D., Sollitto, M., Fedrigo, O., Formenti, G., Jarvis, E.D., Gerdol, M., Ciofi, C., Trucchi, E., Bertorelle, G. :

A high-quality reference genome for the critically endangered Aeolian wall lizard, Podarcis raffonei. J Hered 114:279-285, 2023. Pubmed reference: 36866448. DOI: 10.1093/jhered/esad014.

Poecilia reticulata (guppy) :

2024

Charlesworth, D., Qiu, S., Bergero, R., Gardner, J., Keegan, K., Yong, L., Hastings, A., Konczal, M. :

Has recombination changed during the recent evolution of the guppy Y chromosome? Genetics 226:iyad198, 2024. Pubmed reference: 37956094. DOI: 10.1093/genetics/iyad198.

Poeciliopsis occidentalis (Sonoran topminnow) :

2023

Mussmann, S.M., Harrison, A.S., Wilson, W.D. :

Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis. Mol Biol Rep 50:4743-4751, 2023. Pubmed reference: 36939964. DOI: 10.1007/s11033-023-08376-7.

Poeciliopsis prolifica (blackstripe livebearer) :

2023

Zhang, Y., Reynoso, Y., Reznick, D., Wang, X. :

Whole genome assembly and annotation of blackstripe livebearer Poeciliopsis prolifica. Genome Biol Evol 15:evad195, 2023. Pubmed reference: 37949830. DOI: 10.1093/gbe/evad195.

Pogona vitticeps (central bearded dragon) :

2025

Guo, Q., Pan, Y., Dai, W., Guo, F., Zeng, T., Chen, W., Mi, Y., Zhang, Y., Shi, S., Jiang, W., Cai, H., Wu, B., Zhou, Y., Wang, Y., Yang, C., Shi, X., Yan, X., Chen, J., Cai, C., Yang, J., Xu, X., Gu, Y., Dong, Y., Li, Q. :

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes. Gigascience 14:giaf079, 2025. Pubmed reference: 40825570. DOI: 10.1093/gigascience/giaf079.

Patel, H.R., Alreja, K., Reis, A.L.M., Chang, J.K., Chew, Z.A., Jung, H., Hammond, J.M., Deveson, I.W., Ruiz-Herrera, A., Marin-Gual, L., Holleley, C.E., Zhang, X., Lister, N.C., Whiteley, S., Xiong, L., Dissanayake, D.S.B., Waters, P.D., Georges, A. :

A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps. Gigascience 14:giaf085, 2025. Pubmed reference: 40825569. DOI: 10.1093/gigascience/giaf085.

Pogonophryne albipinna :

2023

Jo, E., Choi, S., Lee, S.J., Kim, J., Choi, E.K., Cho, M., Kim, J., Chung, S., Lee, J., Kim, J.H., Park, H. :

Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna. Sci Data 10:891, 2023. Pubmed reference: 38086886. DOI: 10.1038/s41597-023-02811-x.

Polypterus senegalus (gray bichir) :

2025

Shin, J.W., Kim, B.M., Kim, J., Rhee, J.S. :

Assembly of a high-quality Polypterus senegalus diploid genome. Genes Genomics 47:1187-1197, 2025. Pubmed reference: 41037209. DOI: 10.1007/s13258-025-01685-0.

Pongo :

2025

Han, S., Riyahi, S., Huang, X., Kuhlwilm, M. :

A curated dataset of great ape genome diversity. Sci Data 12:1835, 2025. Pubmed reference: 41261097. DOI: 10.1038/s41597-025-06124-z.

Pongo abelii (Sumatran orangutan) :

2025

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Pongo pygmaeus (Bornean orangutan) :

2025

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Porphyrio hochstetteri (South Island takahe) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

Porphyrio melanotus (Australian swamphen) :

2024

Gaspar, J., Trewick, S.A., Gibb, G.C. :

De-novo assembly of four rail (Aves: Rallidae) genomes: A resource for comparative genomics. Ecol Evol 14:e11694, 2024. Pubmed reference: 39026944. DOI: 10.1002/ece3.11694.

Prasinohaema aff. flavipes (green-blooded skink) :

2025

Probst, T.S., Davis, D.D., Whiting, A.S., Frandsen, P.B. :

The first de novo genome assembly and annotation of a green-blooded skink (Prasinohaema aff. flavipes) from a historic museum sample. J Hered 116:653-662, 2025. Pubmed reference: 40119717. DOI: 10.1093/jhered/esaf014.

Prionailurus bengalensis (leopard cat) :

2020

Bredemeyer, K.R., Harris, A.J., Li, G., Zhao, L., Foley, N.M., Roelke-Parker, M., O'Brien, S.J., Lyons, L.A., Warren, W.C., Murphy, W.J. :

Prionailurus viverrinus (fishing cat) :

2024

Carroll, R.A., Rice, E.S., Murphy, W.J., Lyons, L.A., Thibaud-Nissen, F., Coghill, L.M., Swanson, W.F., Terio, K.A., Boyd, T., Warren, W.C. :

A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 14:8073, 2024. Pubmed reference: 38580653. DOI: 10.1038/s41598-024-56003-7.

Pristella maxillaris :

2025

Bian, C., Hu, C., He, Z., Li, Z., Shi, Q. :

A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris). Sci Data 12:496, 2025. Pubmed reference: 40128533. DOI: 10.1038/s41597-025-04824-0.

Procambarus clarkii (red swamp crayfish) :

2024

Liao, M., Xu, M., Hu, R., Xu, Z., Bonvillain, C., Li, Y., Li, X., Luo, X., Wang, J., Wang, J., Zhao, S., Gu, Z. :

The chromosome-level genome assembly of the red swamp crayfish Procambarus clarkii. Sci Data 11:885, 2024. Pubmed reference: 39143139. DOI: 10.1038/s41597-024-03718-x.

Procyon lotor (raccoon) :

1993

Stanyon, R., Bigoni, F., Wienberg, J., Hadidian, J. :

A Standardized G-Banded Karyotype for the Raccoon (Procyon lotor) Compared with the Domestic Cat. Bollettino di Zoologia 60:41-45, 1993.

Procypris rabaudi (rock carp) :

2025

Han, X., Li, X., Xu, L., Liu, Q., Su, S., Yao, W., He, W. :

The telomere-to-telomere genome assembly and annotation of the rock carp (Procypris rabaudi). Sci Data 12:781, 2025. Pubmed reference: 40360522. DOI: 10.1038/s41597-025-05066-w.

Wang, Z., Ran, M., Liu, X., Zhou, C., Song, Z. :

Chromosome-level genome assembly of rock carp (Procypris rabaudi). Sci Data 12:914, 2025. Pubmed reference: 40447661. DOI: 10.1038/s41597-025-05248-6.

Protobothrops mucrosquamatus (Chinese habu) :

2023

Niu, X., Lu, H., Shi, M., Wang, S., Zhou, Y., Liu, H. :

Genome assembly and annotation of the Brown-Spotted Pit viper Protobothrops mucrosquamatus. GigaByte 2023:gigabyte97, 2023. Pubmed reference: 38023064. DOI: 10.46471/gigabyte.97.

Protopterus annectens (West African lungfish) :

2024

The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 634:96-103, 2024. Pubmed reference: 39143221. DOI: 10.1038/s41586-024-07830-1.

2023

Zhang, R., Liu, Q., Pan, S., Zhang, Y., Qin, Y., Du, X., Yuan, Z., Lu, Y., Song, Y., Zhang, M., Zhang, N., Ma, J., Zhang, Z., Jia, X., Wang, K., He, S., Liu, S., Ni, M., Liu, X., Xu, X., Yang, H., Wang, J., Seim, I., Fan, G. :

A single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization. Nat Commun 14:5630, 2023. Pubmed reference: 37699889. DOI: 10.1038/s41467-023-41309-3.

Protosalanx chinensis :

2025

Zhou, Y., Wang, C., Wang, B., Xu, D., Zhang, X., Ge, Y., Jiang, S., Tang, F., Chen, C., Li, X., Jian, J., You, Y. :

Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis. Gigascience 14:giaf067, 2025. Pubmed reference: 40669866. DOI: 10.1093/gigascience/giaf067.

[No authors listed] :

Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, PProtosalanx chinensiss. Gigascience 14:giaf066, 2025. Pubmed reference: 40669867. DOI: 10.1093/gigascience/giaf066.

Protosalanx hyalocranius (clearhead icefish) :

2017

Liu, K., Xu, D., Li, J., Bian, C., Duan, J., Zhou, Y., Zhang, M., You, X., You, Y., Chen, J., Yu, H., Xu, G., Fang, D.A., Qiang, J., Jiang, S., He, J., Xu, J., Shi, Q., Zhang, Z., Xu, P. :

Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. Gigascience 6:1-6, 2017. Pubmed reference: 28327943. DOI: 10.1093/gigascience/giw012.

Psammodynastes pulverulentus :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Psephotus varius (mulga parrot) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Pseudaspius leptocephalus (Amur asp) :

2025

Gong, X., Ding, Z., Jiang, H., Wang, C., Qian, Y., Chen, W., Yu, D., Liu, Y., Zheng, L., Yang, L., Geng, L. :

Chromosome-level genome assembly of flathead asp (Pseudaspius leptocephalus). Sci Data 12:321, 2025. Pubmed reference: 39987315. DOI: 10.1038/s41597-025-04661-1.

Pseudocaranx georgianus (silver trevally) :

2021

Catanach, A., Ruigrok, M., Bowatte, D., Davy, M., Storey, R., Valenza-Troubat, N., López-Girona, E., Hilario, E., Wylie, M.J., Chagné, D., Wellenreuther, M. :

The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. BMC Genomics 22:785, 2021. Pubmed reference: 34727894. DOI: 10.1186/s12864-021-08102-2.

Pseudochaenichthys georgianus (South Georgia icefish) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Pseudophryne corroboree (corroboree frog) :

2025

Kosch, T.A., Berger, L., Crawford, A.J., Gilbert, D., Goodall, D., Hunter, D., McFadden, M., Abueg, L., Formenti, G., Collins, J., Tilley, T., Jain, N., O'Toole, B., Whelan, C., Cooke, I., Muffato, M., Yates, B., Fedrigo, O., Balacco, J., Jarvis, E.D., Skerratt, L.F. :

A chromosome-level reference genome for the critically endangered Southern Corroboree frog (Pseudophryne corroboree). Wellcome Open Res 10:228, 2025. Pubmed reference: 40756765. DOI: 10.12688/wellcomeopenres.23820.1.

Pseudopleuronectes yokohamae (marbled flounder) :

2025

Zheng, W., Cui, A., Meng, Z., Zhang, N., Jiang, Y., Zheng, J., Zhao, R., Xu, W., Xu, Y. :

Gap-free telomere-to-telomere genome assembly of marbled flounder (Pseudopleuronectes yokohamae). Sci Data 12:1652, 2025. Pubmed reference: 41107286. DOI: 10.1038/s41597-025-05942-5.

Pseudopodoces humilis (Tibetan ground-tit) :

2025

Da, X., Liu, Y., Jin, X., Lu, X. :

Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies. Sci Data 12:799, 2025. Pubmed reference: 40374627. DOI: 10.1038/s41597-025-05171-w.

Pseudorasbora elongata :

2025

Wang, P., Yin, D., Jiang, M., Xie, L., Liu, J., Chen, Y., Wang, X., Shao, Y., Liu, K. :

A chromosome-level genome assembly and annotation of the Pseudorasbora elongata (Cypriniformes: Cyprinidae). Sci Data 12:554, 2025. Pubmed reference: 40169578. DOI: 10.1038/s41597-025-04890-4.

Pseudoryx nghetinhensis (saola) :

2025

Garcia-Erill, G., Liu, S., Le, M.D., Hurley, M.M., Nguyen, H.D., Nguyen, D.Q., Nguyen, D.H., Santander, C.G., Sánchez Barreiro, F., Gomes Martins, N.F., Hanghøj, K., Salleh, F.M., Ramos-Madrigal, J., Wang, X., Sinding, M.S., Morales, H.E., Stæger, F.F., Wilkinson, N., Meng, G., Pečnerová, P., Yang, C., Rasmussen, M.S., Schubert, M., Dunn, R.R., Moltke, I., Zhang, G., Chen, L., Wang, W., Cao, T.T., Nguyen, H.M., Siegismund, H.R., Albrechtsen, A., Gilbert, M.T.P., Heller, R. :

Genomes of critically endangered saola are shaped by population structure and purging. Cell 188:3102-3116.e22, 2025. Pubmed reference: 40328258. DOI: 10.1016/j.cell.2025.03.040.

Pteromys volans (Siberian flying squirrel) :

2025

Wehrenberg, G., Kiebler, A., Greve, C., Beltrán-Sanz, N., Ben Hamadou, A., Meißner, R., Winter, S., Prost, S. :

A prelude to conservation genomics: First chromosome-level genome assembly of a flying squirrel (Pteromyini: Pteromys volans). Ecol Evol 15:e71905, 2025. Pubmed reference: 40900724. DOI: 10.1002/ece3.71905.

Pteronotus parnellii (Parnell's mustached bat) :

2024

Sánchez-de la Vega, G., Gasca-Pineda, J., Martínez-Cárdenas, A., Vernes, S.C., Teeling, E.C., Mai, M., Aguirre-Planter, E., Eguiarte, L.E., Phillips, C.D., Ortega, J. :

The genome sequence of the endemic Mexican common mustached bat, Pteronotus mexicanus. Miller, 1902 [Mormoopidae; Pteronotus]. Gene 929:148821, 2024. Pubmed reference: 39111456. DOI: 10.1016/j.gene.2024.148821.

Pteronura brasiliensis (giant otter) :

2019

Beichman, A.C., Koepfli, K.P., Li, G., Murphy, W., Dobrynin, P., Kliver, S., Tinker, M.T., Murray, M.J., Johnson, J., Lindblad-Toh, K., Karlsson, E.K., Lohmueller, K.E., Wayne, R.K. :

Pterygoplichthys pardalis (Amazon sailfin catfish) :

2025

Lv, Y., Li, Y., Fang, M., Liu, Y., Wang, Y., Yang, Y., Zou, Y., Shi, Q., Mu, X. :

Chromosome-level genome assembly reveals adaptive evolution of the invasive Amazon sailfin catfish (Pterygoplichthys pardalis). Commun Biol 8:616, 2025. Pubmed reference: 40240788. DOI: 10.1038/s42003-025-08029-4.

Xia, W., Xu, H., Liu, Y., Jiang, H., Shi, J., Wu, Y., Yu, Y., Li, X., Fan, W., Zhang, Y., Xu, L. :

Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis. Sci Data 12:1091, 2025. Pubmed reference: 40595666. DOI: 10.1038/s41597-025-05273-5.

Ptyas mucosa (Dhaman) :

2023

Wang, J., Wang, S., Huang, S., Wang, Q., Lan, T., Jiang, M., Wu, H., Yuan, Y. :

The genome assembly and annotation of the Oriental rat snake Ptyas mucosa. GigaByte 2023:gigabyte92, 2023. Pubmed reference: 37753478. DOI: 10.46471/gigabyte.92.

Ptychidio jordani (ratmouth barbel) :

2024

Wang, Y., Yang, Y., Wu, Y., Liu, Y., Li, Q., Liu, C., Jiang, Z., Jiang, W., Chen, F., Mu, X. :

Chromosome-level genome assembly of the ratmouth barbel, Ptychidio jordani. Sci Data 11:1435, 2024. Pubmed reference: 39725708. DOI: 10.1038/s41597-024-04331-8.

Ptychocheilus lucius (Colorado pikeminnow) :

2024

Mussmann, S.M. :

Assembly and annotation of a chromosome-level reference genome for the endangered Colorado pikeminnow Ptychocheilus lucius. G3 (Bethesda) 14:jkae217, 2024. Pubmed reference: 39268723. DOI: 10.1093/g3journal/jkae217.

Puffinus mauretanicus :

2024

Corominas, M., Marquès-Bonet, T., Arnedo, M.A., Bayés, M., Belmonte, J., Escrivà, H., Fernández, R., Gabaldón, T., Garnatje, T., Germain, J., Niell, M., Palero, F., Pons, J., Puigdomènech, P., Initiative For The Earth BioGenome Project, T.C. :

The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR Genom Bioinform 6:lqae075, 2024. Pubmed reference: 39022326. DOI: 10.1093/nargab/lqae075.

Puma concolor (puma) :

2024

Supple, M.A., Escalona, M., Alexandre, N., Buchalski, M.R., Riley, S.P.D., Dellinger, J.A., Vickers, T.W., Sahasrabudhe, R., Nguyen, O., Fairbairn, C.W., Seligmann, W.E., Wilmers, C.C., Shapiro, B. :

A chromosome-level genome assembly of the mountain lion, Puma concolor. J Hered 116:479-487, 2024. Pubmed reference: 39506490. DOI: 10.1093/jhered/esae063.

Pungitius pungitius (ninespine stickleback) :

2024

Wang, D., Rastas, P., Yi, X., Löytynoja, A., Kivikoski, M., Feng, X., Reid, K., Merilä, J. :

Improved assembly of the Pungitius pungitius reference genome. G3 (Bethesda) 14:jkae126, 2024. Pubmed reference: 38861393. DOI: 10.1093/g3journal/jkae126.

Puntigrus tetrazona (Sumatra barb) :

2021

Li, J.T., Wang, Q., Huang Yang, M.D., Li, Q.S., Cui, M.S., Dong, Z.J., Wang, H.W., Yu, J.H., Zhao, Y.J., Yang, C.R., Wang, Y.X., Sun, X.Q., Zhang, Y., Zhao, R., Jia, Z.Y., Wang, X.Y. :

Pusa sibirica (Baikal seal) :

2023

Yakupova, A., Tomarovsky, A., Totikov, A., Beklemisheva, V., Logacheva, M., Perelman, P.L., Komissarov, A., Dobrynin, P., Krasheninnikova, K., Tamazian, G., Serdyukova, N.A., Rayko, M., Bulyonkova, T., Cherkasov, N., Pylev, V., Peterfeld, V., Penin, A., Balanovska, E., Lapidus, A. :

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes (Basel) 14:619, 2023. Pubmed reference: 36980891. DOI: 10.3390/genes14030619.

Python regius (ball python) :

2025

Hunt, D.R., Allen, H., Martin, T.G., Feghali, S.N., Chuong, E.B., Leinwand, L.A. :

Genome Report: First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity. bioRxiv , 2025. Pubmed reference: 39975114. DOI: 10.1101/2025.02.01.635752.

Hunt, D.R., Allen, H., Martin, T.G., Feghali, S.N., Chuong, E.B., Leinwand, L.A. :

Genome Report: First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity. G3 (Bethesda) 15:jkaf197, 2025. Pubmed reference: 40891283. DOI: 10.1093/g3journal/jkaf197.

Quiscalus major :

2025

Corbett, E.C., Moncrieff, A.E., Brumfield, R.T., Faircloth, B.C. :

A reference genome for boat-tailed grackles (Quiscalus major). J Hered 116:540-547, 2025. Pubmed reference: 40272064. DOI: 10.1093/jhered/esaf019.

Rallus crepitans (clapper rail) :

2023

Elizondo, E.C., Faircloth, B.C., Brumfield, R.T., Shakya, S.B., Ellis, V.A., Schmidt, C.J., Kovach, A.I., Shriver, W.G. :

A high quality de novo genome assembly for clapper rail (Rallus crepitans). G3 (Bethesda) 13:jkad097, 2023. Pubmed reference: 37130071. DOI: 10.1093/g3journal/jkad097.

Rallus limicola :

2023

Hall, L.A., Wang, I.J., Escalona, M., Beraut, E., Sacco, S., Sahasrabudhe, R., Nguyen, O., Toffelmier, E., Shaffer, H.B., Beissinger, S.R. :

Reference genome of the Virginia rail, Rallus limicola. J Hered 114:428-435, 2023. Pubmed reference: 37105531. DOI: 10.1093/jhered/esad026.

Rangifer tarandus (reindeer) :

2025

Tørresen, O.K., Tooming-Klunderud, A., Skage, M., Streitlien, A.E., Strand, O., Rolandsen, C.M., Ferrari, G., Cerca, J., Mysterud, A., Jakobsen, K.S. :

Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus). J Hered :esaf094, 2025. Pubmed reference: 41182255. DOI: 10.1093/jhered/esaf094.

2024

Yi, W., Hu, M., Shi, L., Li, T., Sun, H., Qin, L., Yan, S. :

Analysis of genetic variants in protein-coding genes of Aoluguya reindeer based on the whole-genome data. Anim Genet 55:296-298, 2024. Pubmed reference: 38319118. DOI: 10.1111/age.13402.

Wu, B., Ren, Q., Yan, X., Zhao, F., Qin, T., Xin, P., Cui, X., Wang, K., Du, R., Røed, K.H., Côté, S.D., Yannic, G., Li, Z., Qiu, Q. :

Resequencing of reindeer genomes provides clues to their docile habits. Evol Lett 8:494-504, 2024. Pubmed reference: 39100238. DOI: 10.1093/evlett/qrae006.

2023

Poisson, W., Prunier, J., Carrier, A., Gilbert, I., Mastromonaco, G., Albert, V., Taillon, J., Bourret, V., Droit, A., Côté, S.D., Robert, C. :

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 24:142, 2023. Pubmed reference: 36959567. DOI: 10.1186/s12864-023-09189-5.

Shi, L., Shi, Z., Hu, M., Wu, M., Quan, X., Qin, L., Zhao, Z., Sun, H., Tian, L., Yan, S. :

Whole genome sequencing of Aoluguya reindeer (Rangifer tarandus) in China. Front Genet 14:1243795, 2023. Pubmed reference: 37600663. DOI: 10.3389/fgene.2023.1243795.

Pokharel, K., Weldenegodguad, M., Dudeck, S., Honkatukia, M., Lindeberg, H., Mazzullo, N., Paasivaara, A., Peippo, J., Soppela, P., Stammler, F., Kantanen, J. :

Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 13:23019, 2023. Pubmed reference: 38155192. DOI: 10.1038/s41598-023-50253-7.

2022

Carrier, A., Prunier, J., Poisson, W., Trottier-Lavoie, M., Gilbert, I., Cavedon, M., Pokharel, K., Kantanen, J., Musiani, M., Côté, S.D., Albert, V., Taillon, J., Bourret, V., Droit, A., Robert, C. :

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 23:687, 2022. Pubmed reference: 36199020. DOI: 10.1186/s12864-022-08899-6.

1995

Røed, K.H., Jacobsen, M. :

Chromosome aberrations in Norwegian reindeer following the Chernobyl accident. Mutat Res 346:159-65, 1995. Pubmed reference: 7700280. DOI: 10.1016/0165-7992(95)90048-9.

1993

Gripenberg, U., Wessman, M. :

Restriction Endonuclease Staining Profiles in the C- Heterochromatin of Cervidae. Hereditas 118:251-257, 1993.

Ranitomeya imitator (mimic poison frog) :

2024

Stuckert, A.M.M., Chouteau, M., McClure, M., LaPolice, T.M., Linderoth, T., Nielsen, R., Summers, K., MacManes, M.D. :

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Mol Ecol 33:e17438, 2024. Pubmed reference: 38923007. DOI: 10.1111/mec.17438.

Ranoidea serrata (green-eyed treefrog) :

2023

Bertola, L.V., Hoskin, C.J., Jones, D.B., Zenger, K.R., McKnight, D.T., Higgie, M. :

The first linkage map for Australo-Papuan treefrogs (family: Pelodryadidae) reveals the sex-determination system of the green-eyed treefrog (Litoria serrata). Heredity (Edinb) 131:263-272, 2023. Pubmed reference: 37542195. DOI: 10.1038/s41437-023-00642-5.

Rhabdophis nuchalis (Hubei keelback) :

2024

Duan, M., Yang, S., Li, X., Tang, X., Cheng, Y., Luo, J., Wang, J., Song, H., Wang, Q., Zhu, G.X. :

Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 11:850, 2024. Pubmed reference: 39117633. DOI: 10.1038/s41597-024-03708-z.

Rhabdosargus sarba (goldlined seabream) :

2025

Shekhar, M.S., Katneni, V.K., Jangam, A.K., Krishnan, K., Prabhudas, S.K., Raymond, J.J.A., Lal, K.K. :

Chromosome-level genome assembly with telomeric repeats at scaffold ends for Rhabdosargus sarba. Sci Data 12:1202, 2025. Pubmed reference: 40645974. DOI: 10.1038/s41597-025-05324-x.

Rhinatrema bivittatum (two-lined caecilian) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Rhinogobio nasutus :

2025

Jiang, C., Du, Y., Lou, Z., Zhang, Y., Wang, T. :

Telomere-to-telomere reference genome of Rhinogobio nasutus, an endangered endemic fish from the Yellow River. Sci Data 12:462, 2025. Pubmed reference: 40113806. DOI: 10.1038/s41597-025-04793-4.

Rhinogobio ventralis :

2025

Chen, J., Zhang, X., Li, Y., Lv, Y., You, X., Shi, Q., Wen, Z. :

Chromosome-scale genome assembly and genome-wide identification of antimicrobial peptide-containing genes in the endangered long-finned gudgeon fish (Rhinogobio ventralis). Biology (Basel) 14:1486, 2025. Pubmed reference: 41300277. DOI: 10.3390/biology14111486.

Rhinogobius duospilus (white cheek goby) :

2025

Wu, L., Hu, J., Zhang, S., Fam, Y.Q., Xia, J., Li, C. :

High-quality genome assembly and annotation of the white cheeked goby, Rhinogobius duospilus (Herre, 1935) (Gobiiformes: Oxudercidae). G3 (Bethesda) :jkaf278, 2025. Pubmed reference: 41248690. DOI: 10.1093/g3journal/jkaf278.

Rhinolophus affinis (intermediate horseshoe bat) :

2024

Zhao, L., Yuan, J., Wang, G., Jing, H., Huang, C., Xu, L., Xu, X., Sun, T., Chen, W., Mao, X., Li, G. :

Chromosome-level genome and population genomics of the intermediate horseshoe bat (Rhinolophus affinis) reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation. Zool Res 45:2095-8137(2024)05-1147-14:1147-1160, 2024. Pubmed reference: 39257377. DOI: 10.24272/j.issn.2095-8137.2024.027.

Rhinolophus ferrumequinum (greater horseshoe bat) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

Rhinolophus rex :

2024

Lan, L., Zhang, X., Yang, S., Mao, X., Dong, J. :

Chromosome-level genome assembly of the king horseshoe bat (Rhinolophus rex) provides insights into its conservation status and chromosomal evolution of Rhinolophus. J Hered 116:499-512, 2024. Pubmed reference: 39679954. DOI: 10.1093/jhered/esae077.

Rhomboplites aurorubens :

2025

Roa-Varón, A., Moulos, P., Harter, S., David, A., Quattrini, A.M., Herrera, S. :

Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens). Sci Data 12:1281, 2025. Pubmed reference: 40701987. DOI: 10.1038/s41597-025-05573-w.

Rhyacichthys aspro (loach goby) :

2025

Wang, T.Y., Wu, Y.W., Lu, H.J., Liao, T.Y., Tai, J.H., Huang, S.P., Wang, F.Y., Yu, T.H., Ting, C.T., Chaw, S.M., Wang, H.Y. :

Chromosome-level genome assembly of the loach goby Rhyacichthys aspro offers insights into gobioidei evolution. Mol Ecol Resour 25:e14110, 2025. Pubmed reference: 40168108. DOI: 10.1111/1755-0998.14110.

Rhynchocypris lagowskii (Amur minnow) :

2025

Bai, X., Li, H., Wang, Y., Zhang, X., Li, J., Luo, X., Luo, Z., Ma, L., Hao, S., Wu, C., Zhang, W. :

Chromosome-level genome assembly of Amur Minnow (Rhynchocypris lagowskii). Sci Data 12:1669, 2025. Pubmed reference: 41125655. DOI: 10.1038/s41597-025-05905-w.

Rissa tridactyla (black-legged kittiwake) :

2023

Sozzoni, M., Ferrer Obiol, J., Formenti, G., Tigano, A., Paris, J.R., Balacco, J.R., Jain, N., Tilley, T., Collins, J., Sims, Y., Wood, J., Benowitz-Fredericks, Z.M., Field, K.A., Seyoum, E., Gatt, M.C., Léandri-Breton, D.J., Nakajima, C., Whelan, S., Gianfranceschi, L., Hatch, S.A., Elliott, K.H., Shoji, A., Cecere, J.G., Jarvis, E.D., Pilastro, A., Rubolini, D. :

A chromosome-level reference genome for the black-legged kittiwake (Rissa tridactyla), a declining circumpolar seabird. Genome Biol Evol 15:evad153, 2023. Pubmed reference: 37590950. DOI: 10.1093/gbe/evad153.

Rusa alfredi (Visayan spotted deer) :

2025

Javier, M.C.F., Noblezada, A.C., Sienes, P.M.Q., Guino-O, R.S., Palomar-Abesamis, N., Malay, M.C.D., Del Castillo, C.S., Ferriols, V.M.E.N. :

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species. GigaByte 2025:gigabyte150, 2025. Pubmed reference: 40041424. DOI: 10.46471/gigabyte.150.

Saccostrea glomerata :

2018

Powell, D., Subramanian, S., Suwansa-Ard, S., Zhao, M., O'Connor, W., Raftos, D., Elizur, A. :

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves. DNA Res 25:655-665, 2018. Pubmed reference: 30295708. DOI: 10.1093/dnares/dsy032.

Sagmatias cruciger (hourglass dolphin) :

2025

McGrath, N., le Roux, J., Whibley, A., Alexander, A., Stewart, R.O., Johnstone, M., Stockin, K.A., Silander, O.K. :

A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome. G3 (Bethesda) 15:jkaf044, 2025. Pubmed reference: 40036857. DOI: 10.1093/g3journal/jkaf044.

Salamandra salamandra (fire salamander) :

2023

Libro, P., Chiocchio, A., De Rysky, E., Di Martino, J., Bisconti, R., Castrignanò, T., Canestrelli, D. :

De novo transcriptome assembly and annotation for gene discovery in Salamandra salamandra at the larval stage. Sci Data 10:330, 2023. Pubmed reference: 37244908. DOI: 10.1038/s41597-023-02217-9.

Salaria pavo (peacock blenny) :

2024

Cardoso, S.D., Jiang, C., Sun, L., Zhang, L., Gonçalves, D. :

Chromosome-level genome assembly of the highly-polymorphic peacock blenny (Salaria pavo). Sci Data 11:1424, 2024. Pubmed reference: 39715741. DOI: 10.1038/s41597-024-04242-8.

Salmo salar (Atlantic salmon) :

2025

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Johansson, H., Erkinaro, J., Falkegård, M., Foldvik, A., Orell, P., Primmer, C.R., Pritchard, V.L. :

A single nucleotide polymorphism genotyping panel for efficient genetic stock identification of the Teno river Atlantic salmon (Salmo salar) population complex. J Fish Biol , 2025. Pubmed reference: 40890907. DOI: 10.1111/jfb.70179.

2023

MacLeod-Bigley, M.L., Boulding, E.G. :

High-density linkage maps detail sex-specific regions of suppressed recombination near fusions of polymorphic chromosomes in purebred and hybrid North American Atlantic salmon (Salmo salar). Genome 66:175-192, 2023. Pubmed reference: 36944224. DOI: 10.1139/gen-2022-0065.

Gao, G., Waldbieser, G.C., Youngblood, R.C., Zhao, D., Pietrak, M.R., Allen, M.S., Stannard, J.A., Buchanan, J.T., Long, R.L., Milligan, M., Burr, G., Mejía-Guerra, K., Sheehan, M.J., Scheffler, B.E., Rexroad, C.E., Peterson, B.C., Palti, Y. :

The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50 K SNP array for the St John River aquaculture strain of North American Atlantic salmon. G3 (Bethesda) 13:jkad138, 2023. Pubmed reference: 37335943. DOI: 10.1093/g3journal/jkad138.

2016

Lien, S., Koop, B.F., Sandve, S.R., Miller, J.R., Kent, M.P., Nome, T., Hvidsten, T.R., Leong, J.S., Minkley, D.R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R.A., von Schalburg, K., Rondeau, E.B., Di Genova, A., Samy, J.K., Olav Vik, J., Vigeland, M.D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., de Jong, P., Moen, T., Baranski, M., Palti, Y., Smith, D.R., Yorke, J.A., Nederbragt, A.J., Tooming-Klunderud, A., Jakobsen, K.S., Jiang, X., Fan, D., Hu, Y., Liberles, D.A., Vidal, R., Iturra, P., Jones, S.J., Jonassen, I., Maass, A., Omholt, S.W., Davidson, W.S. :

The Atlantic salmon genome provides insights into rediploidization. Nature 533:200-5, 2016. Pubmed reference: 27088604. DOI: 10.1038/nature17164.

2014

Houston, R.D., Taggart, J.B., Cézard, T., Bekaert, M., Lowe, N.R., Downing, A., Talbot, R., Bishop, S.C., Archibald, A.L., Bron, J.E., Penman, D.J., Davassi, A., Brew, F., Tinch, A.E., Gharbi, K., Hamilton, A. :

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). BMC Genomics 15:90, 2014. Pubmed reference: 24524230. DOI: 10.1186/1471-2164-15-90.

Gonen, S., Lowe, N.R., Cezard, T., Gharbi, K., Bishop, S.C., Houston, R.D. :

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing. BMC Genomics 15:166, 2014. Pubmed reference: 24571138. DOI: 10.1186/1471-2164-15-166.

Salmo trutta (brown trout) :

2025

Li, C., Han, S., Li, S., Liu, K., Liu, Y., Wang, H.Y., Wang, Q., Liu, C., Shao, C. :

Near complete genome assembly of Yadong trout (Salmo trutta). Sci Data 12:74, 2025. Pubmed reference: 39814780. DOI: 10.1038/s41597-025-04418-w.

2019

Saint-Pé, K., Leitwein, M., Tissot, L., Poulet, N., Guinand, B., Berrebi, P., Marselli, G., Lascaux, J.M., Gagnaire, P.A., Blanchet, S. :

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics 20:582, 2019. Pubmed reference: 31307373. DOI: 10.1186/s12864-019-5958-9.

2017

Leitwein, M., Guinand, B., Pouzadoux, J., Desmarais, E., Berrebi, P., Gagnaire, P.A. :

A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity. G3 (Bethesda) 7:1365-1376, 2017. Pubmed reference: 28235829. DOI: 10.1534/g3.116.038497.

Salmonidae (salmonids) :

1996

Abuín, M., Martínez, P., Sánchez, L. :

G-like banding pattern in two salmonid species: Oncorhynchus mykiss and Oncorhynchus kisutch. Chromosome Res 4:471-3, 1996. Pubmed reference: 8889247. DOI: 10.1007/BF02265055.

1988

Mayr, B., Kalat, M., Rab, P. :

Heterochromatins and band karyotypes in three species of salmonids. Theor Appl Genet 76:45-53, 1988. Pubmed reference: 24231981. DOI: 10.1007/BF00288830.

1987

Hartley, S.E. :

The chromosomes of salmonid fishes. Biological reviews of the Cambridge Philosophical Society 62:197-214, 1987.

1986

Phillips, R.B., Zajicek, K.D., Utter, F.M. :

Chromosome banding in salmonid fishes: nucleolar organizer regions in Oncorhynchus. Can J Genet Cytol 28:502-10, 1986. Pubmed reference: 3756608. DOI: 10.1139/g86-074.

Salvelinus alpinus (Arctic char) :

2025

Kurta, K., Fedi, M.O., Baker, K., Barker, T., Catchpole, L., Ciofi, C., Cocco, A., Collins, J., Diedericks, G., Diroma, M.A., Durrant, A., Hindar, K., Iannucci, A., Irish, N., Knitlhoffer, V., Laikre, L., Leitão, H.G., Lucchini, S., McTaggart, S., Pálsson, A., Pettersson, M.E., Ryman, N., Snorrason, S.S., Svardal, H., Swarbreck, D., Waterhouse, R.M., Watkins, C., Wood, J.M.D., Xiao, H., Gharbi, K., Jónsson, Z.O., Andersson, L. :

Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr. Mol Ecol 34:e70085, 2025. Pubmed reference: 40856096. DOI: 10.1111/mec.70085.

2024

[No authors listed] :

Editorial Note: Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus). PLoS One 19:e0304369, 2024. Pubmed reference: 38833497. DOI: 10.1371/journal.pone.0304369.

Beemelmanns, A., Bouchard, R., Michaelides, S., Normandeau, E., Jeon, H.B., Chamlian, B., Babin, C., Hénault, P., Perrot, O., Harris, L.N., Zhu, X., Fraser, D., Bernatchez, L., Moore, J.S. :

2023

Pappas, F., Kurta, K., Vanhala, T., Jeuthe, H., Hagen, Ø., Beirão, J., Palaiokostas, C. :

Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia. Evol Appl 16:797-813, 2023. Pubmed reference: 37124091. DOI: 10.1111/eva.13537.

1991

Hartley, S.E. :

C, Q, and restriction enzyme banding of the chromosomes in brook trout (Salvelinus fontinalis) and Arctic charr (Salvelinus alpinus). Hereditas 114:253-61, 1991. Pubmed reference: 1960102. DOI: 10.1111/j.1601-5223.1991.tb00332.x.

Salvelinus fontinalis (brook trout) :

2025

Lecomte, L., Ferchaud, A.L., Normandeau, E., Mérot, C., Langlois-Parisé, I., Therrien, J.C., Bérubé, P., Djambazian, H., Nawarathna, P.M., Ragoussis, J., Fraser, D. :

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis). G3 (Bethesda) 15:jkaf066, 2025. Pubmed reference: 40130537. DOI: 10.1093/g3journal/jkaf066.

2024

Beemelmanns, A., Bouchard, R., Michaelides, S., Normandeau, E., Jeon, H.B., Chamlian, B., Babin, C., Hénault, P., Perrot, O., Harris, L.N., Zhu, X., Fraser, D., Bernatchez, L., Moore, J.S. :

2023

Mamoozadeh, N.R., Whiteley, A.R., Letcher, B.H., Kazyak, D.C., Tarsa, C., Meek, M.H. :

A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis). Mol Ecol Resour 25:e13853, 2023. Pubmed reference: 37584304. DOI: 10.1111/1755-0998.13853.

1991

Hartley, S.E. :

Salvelinus malma (Dolly Varden) :

2025

Zeng, X., Hu, L., Zhang, J., Yao, Y., Bao, H., Li, D., Gao, Q., Tian, Y. :

The chromosome-level genome assembly and annotation of Salvelinus malma. Sci Data 12:1875, 2025. Pubmed reference: 41315286. DOI: 10.1038/s41597-025-06145-8.

Sarcophilus harrisii (Tasmanian devil) :

2023

Stammnitz, M.R., Gori, K., Kwon, Y.M., Harry, E., Martin, F.J., Billis, K., Cheng, Y., Baez-Ortega, A., Chow, W., Comte, S., Eggertsson, H., Fox, S., Hamede, R., Jones, M., Lazenby, B., Peck, S., Pye, R., Quail, M.A., Swift, K., Wang, J., Wood, J., Howe, K., Stratton, M.R., Ning, Z., Murchison, E.P. :

The evolution of two transmissible cancers in Tasmanian devils. Science 380:283-293, 2023. Pubmed reference: 37079675. DOI: 10.1126/science.abq6453.

Sarcoramphus papa (king vulture) :

2024

Buthasane, W., Shotelersuk, V., Chetruengchai, W., Srichomthong, C., Assawapitaksakul, A., Tangphatsornruang, S., Pootakham, W., Sonthirod, C., Tongsima, S., Wangkumhang, P., Wilantho, A., Thongphakdee, A., Sanannu, S., Poksawat, C., Nipanunt, T., Kasorndorkbua, C., Koepfli, K.P., Pukazhenthi, B.S., Suriyaphol, P., Wongsurawat, T., Jenjaroenpun, P., Suriyaphol, G. :

Comprehensive genome assembly reveals genetic diversity and carcass consumption insights in critically endangered Asian king vultures. Sci Rep 14:9455, 2024. Pubmed reference: 38658744. DOI: 10.1038/s41598-024-59990-9.

Sardinella longiceps (Indian oil sardine) :

2023

Sukumaran, S., Sebastian, W., Gopalakrishnan, A., Mathew, O.K., Vysakh, V.G., Rohit, P., Jena, J.K. :

The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps. Sci Data 10:565, 2023. Pubmed reference: 37626109. DOI: 10.1038/s41597-023-02481-9.

Sarotherodon galilaeus (mango tilapia) :

2023

Fiteha, Y.G., Rashed, M.A., Ali, R.A.M., Magdy, M. :

Characterization and phylogenetic analysis of the complete mitochondrial genome of Mango tilapia (Sarotherodon galilaeus: Cichlidae). Mol Biol Rep 50:3945-3950, 2023. Pubmed reference: 36781609. DOI: 10.1007/s11033-023-08288-6.

Scaptonyx fusicauda (long-tailed mole) :

2023

Wang, X., Liu, Y., Liao, R., Liu, S. :

The complete mitochondrial genome of the long-tailed mole: Scaptonyx fusicaudus (Eulipotyphla, Talpidae). Mitochondrial DNA B Resour 8:264-265, 2023. Pubmed reference: 36816057. DOI: 10.1080/23802359.2022.2032438.

Scarus forsteni (Forsten's parrotfish) :

2024

Liang, Y., Xian, L., Pan, J., Zhu, K., Guo, H., Liu, B., Zhang, N., Ou-Yang, Y., Zhang, Q., Zhang, D. :

De novo genome assembly of the Whitespot Parrotfish (Scarus forsteni): A valuable scaridae genomic resource. Genes (Basel) 15:249, 2024. Pubmed reference: 38397238. DOI: 10.3390/genes15020249.

Sceloporus occidentalis (western fence lizard) :

2023

Bishop, A.P., Westeen, E.P., Yuan, M.L., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Chumchim, N., Toffelmier, E., Fisher, R.N., Shaffer, H.B., Wang, I.J. :

Assembly of the largest squamate reference genome to date: the western fence lizard, Sceloporus occidentalis. J Hered 114:521-528, 2023. Pubmed reference: 37335574. DOI: 10.1093/jhered/esad037.

Schizothorax macropogon :

2024

Liang, X., Wang, W., Huang, J., Luo, M., Wangdui, N., Sun, C., Lu, J. :

A chromosome-level genome assembly of big-barbel schizothorcin, Schizothorax macropogon. Sci Data 11:1402, 2024. Pubmed reference: 39702420. DOI: 10.1038/s41597-024-04266-0.

Sciaenops ocellatus (red drum) :

2023

Xiao, Y., Liu, J., Wei, J., Xiao, Z., Li, J., Ma, Y. :

Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration. Sci Data 10:774, 2023. Pubmed reference: 37935724. DOI: 10.1038/s41597-023-02699-7.

Sciurus niger (fox squirrel) :

2021

Kang, L., Michalak, P., Hallerman, E., Moncrief, N.D. :

A draft genome assembly for the Eastern fox squirrel, Sciurus niger. G3 (Bethesda) 11:jkab315, 2021. Pubmed reference: 34550334. DOI: 10.1093/g3journal/jkab315.

Scolopax rusticola (Eurasian woodcock) :

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

Scomber colias (Atlantic chub mackerel) :

2022

Machado, A.M., Gomes-Dos-Santos, A., Fonseca, M.M., da Fonseca, R.R., Veríssimo, A., Felício, M., Capela, R., Alves, N., Santos, M., Salvador-Caramelo, F., Domingues, M., Ruivo, R., Froufe, E., Castro, L.F.C. :

A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource. GigaByte 2022:gigabyte40, 2022. Pubmed reference: 36824513. DOI: 10.46471/gigabyte.40.

Scomber japonicus (chub mackerel) :

2023

Lee, Y.H., Abueg, L., Kim, J.K., Kim, Y.W., Fedrigo, O., Balacco, J., Formenti, G., Howe, K., Tracey, A., Wood, J., Thibaud-Nissen, F., Nam, B.H., No, E.S., Kim, H.R., Lee, C., Jarvis, E.D., Kim, H. :

Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean. Sci Data 10:880, 2023. Pubmed reference: 38066002. DOI: 10.1038/s41597-023-02782-z.

Scomber scombrus (Atlantic mackerel) :

2024

Manuzzi, A., Aguirre-Sarabia, I., Díaz-Arce, N., Bekkevold, D., Jansen, T., Gomez-Garrido, J., Alioto, T.S., Gut, M., Castonguay, M., Sanchez-Maroño, S., Álvarez, P., Rodriguez-Ezpeleta, N. :

Atlantic mackerel population structure does not support genetically distinct spawning components. Open Res Eur 4:82, 2024. Pubmed reference: 39524113. DOI: 10.12688/openreseurope.17365.1.

Scomberomorus guttatus (Indo-Pacific king mackerel) :

2024

Gao, Y., Liu, S., Gutang, Q., Li, C., Lin, X., Liang, B., Li, P., Lin, J., Liu, W. :

Chromosome-level genome assembly of Indo-Pacific king mackerel (Scomberomorus guttatus). Sci Data 11:1224, 2024. Pubmed reference: 39537638. DOI: 10.1038/s41597-024-04110-5.

Scotinomys teguina (Alston's brown mouse) :

2023

Smith, S.K., Frazel, P.W., Khodadadi-Jamayran, A., Zappile, P., Marier, C., Okhovat, M., Brown, S., Long, M.A., Heguy, A., Phelps, S.M. :

De novo assembly and annotation of the singing mouse genome. BMC Genomics 24:569, 2023. Pubmed reference: 37749493. DOI: 10.1186/s12864-023-09678-7.

Scyliorhinus canicula (smaller spotted catshark) :

2024

Mayeur, H., Leyhr, J., Mulley, J., Leurs, N., Michel, L., Sharma, K., Lagadec, R., Aury, J.M., Osborne, O.G., Mulhair, P., Poulain, J., Mangenot, S., Mead, D., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Dolucan, J., Dudchenko, O., Omer, A.D., Weisz, D., Aiden, E.L., McCarthy, S., Sims, Y., Torrance, J., Tracey, A., Howe, K., Baril, T., Hayward, A., Martinand-Mari, C., Sanchez, S., Haitina, T., Martin, K., Korsching, S.I., Mazan, S., Debiais-Thibaud, M. :

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. bioRxiv , 2024. Pubmed reference: 39005470. DOI: 10.1101/2024.05.23.595469.

Mayeur, H., Leyhr, J., Mulley, J., Leurs, N., Michel, L., Sharma, K., Lagadec, R., Aury, J.M., Osborne, O.G., Mulhair, P., Poulain, J., Mangenot, S., Mead, D., Smith, M., Corton, C., Olive, K., Skelton, J., Betteridge, E., Dolucan, J., Dudchenko, O., Omer, A.D., Weisz, D., Aiden, E.L., McCarthy, S., Sims, Y., Torrance, J., Tracey, A., Howe, K., Baril, T., Hayward, A., Martinand-Mari, C., Sanchez, S., Haitina, T., Martin, K., Korsching, S.I., Mazan, S., Debiais-Thibaud, M. :

The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. Mol Biol Evol 41:msae246, 2024. Pubmed reference: 39657112. DOI: 10.1093/molbev/msae246.

Sebastes paucispinis (bocaccio) :

2025

De-Kayne, R., Li, S., Escalona, M., Lou, R.N., Owens, G.L., Kolora, S.R.R., Jainese, C., Seeto, K., McCrea, M., Nguyen, O., Chumchim, N., Sahasrabudhe, R.M., Fairbairn, C.W., Green, R.E., Seligmann, W.E., Love, M., Sudmant, P.H. :

A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis. J Hered 116:826-834, 2025. Pubmed reference: 40323688. DOI: 10.1093/jhered/esaf026.

[No authors listed] :

Correction to: A haplotype-resolved genome assembly of the bocaccio rockfish. J Hered :esaf078, 2025. Pubmed reference: 41059922. DOI: 10.1093/jhered/esaf078.

Semaprochilodus insignis :

2023

Yang, X., Song, Y., Zhang, R., Yu, M., Guo, X., Guo, H., Du, X., Sun, S., Li, C., Mao, X., Fan, G., Liu, X. :

Semicossyphus pulcher :

2022

Bernardi, G., DeBiasse, M., Escalona, M., Marimuthu, M.P.A., Nguyen, O., Sacco, S., Beraut, E., Miller, C., Toffelmier, E., Shaffer, H.B. :

Reference genome of the California sheephead, Semicossyphus pulcher (Labridae, Perciformes), a keystone fish predator in kelp forest ecosystems. J Hered 113:649-656, 2022. Pubmed reference: 35778264. DOI: 10.1093/jhered/esac032.

Semotilus atromaculatus (creek chub) :

2024

Meuser, A.V., Pitura, A.R., Mandeville, E.G. :

A high-quality reference genome for the common creek chub, Semotilus atromaculatus. G3 (Bethesda) 14:jkad283, 2024. Pubmed reference: 38128526. DOI: 10.1093/g3journal/jkad283.

Serinus canaria (common canary) :

2025

Madison, F.N., Conte, M.A., Brown, J.A., Carleton, K.L., Dooling, R.J. :

Whole genome sequencing identifies genetic candidates for high-frequency hearing loss in canaries (serinus canaria). J Acoust Soc Am 157:2330-2335, 2025. Pubmed reference: 40167343. DOI: 10.1121/10.0036218.

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

Seriola lalandi (yellowtail amberjack) :

2021

Li, S., Liu, K., Cui, A., Hao, X., Wang, B., Wang, H.Y., Jiang, Y., Wang, Q., Feng, B., Xu, Y., Shao, C., Liu, X. :

A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi). Front Genet 12:825742, 2021. Pubmed reference: 35126476. DOI: 10.3389/fgene.2021.825742.

Serpentes (snakes) :

2024

Roberts, J.R., Bernstein, J.M., Austin, C.C., Hains, T., Mata, J., Kieras, M., Pirro, S., Ruane, S. :

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics. J Hered 115:487-497, 2024. Pubmed reference: 38722259. DOI: 10.1093/jhered/esae026.

Setipinna tenuifilis (common hairfin anchovy) :

2024

Liu, B., Li, J., Peng, Y., Zhang, K., Liu, Q., Jin, X., Zheng, S., Wang, Y., Gong, L., Liu, L., Lü, Z., Liu, Y. :

Chromosome-level genome assembly and population genomic analysis reveal evolution and local adaptation in common hairfin anchovy (Setipinna tenuifilis). Mol Ecol 33:e17067, 2024. Pubmed reference: 37434292. DOI: 10.1111/mec.17067.

Setophaga petechia (yellow warbler) :

2024

Tsai, W.L.E., Escalona, M., Garrett, K.L., Terrill, R.S., Sahasrabudhe, R., Nguyen, O., Beraut, E., Seligmann, W., Fairbairn, C.W., Harrigan, R.J., McCormack, J.E., Alfaro, M.E., Smith, T.B., Bay, R.A. :

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia). J Hered 115:317-325, 2024. Pubmed reference: 38401156. DOI: 10.1093/jhered/esae008.

Sibirionetta formosa (Baikal teal) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Siganus canaliculatus (white-spotted rabbitfish) :

2025

Huang, X., Lu, Y., Zhang, H., Xian, L., Huang, S., Yang, Y., Wang, L., Zhang, D., Li, C. :

Chromosome-level genome assembly and annotation of the White-spotted spinefoot Siganus canaliculatus. Sci Data 12:482, 2025. Pubmed reference: 40122978. DOI: 10.1038/s41597-025-04844-w.

Sigmodon hispidus (hispid cotton rat) :

2025

Lilue, J., Corvelo, A., Gómez-Garrido, J., Akagi, K., Yang, F., Green, G., Ng, B.L., Fu, B., Chorostecki, U.P., Warner, S.C., Marcet-Houben, M., Keane, T.M., Mullikin, J.C., Alioto, T., Gabaldón, T., Hubert, B., Symer, D.E., Niewiesk, S. :

A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections. BMC Biol 23:217, 2025. Pubmed reference: 40682131. DOI: 10.1186/s12915-025-02316-6.

Siniperca chuatsi (mandarin fish) :

2025

Han, C., Liu, S., Peng, S., Liu, S., Zeng, J., Chen, J., Lin, H., Li, C., Li, S., Zhang, Y. :

Assembly and analysis of Sinipercidae fish sex chromosomes reveals that a supergene drives sex chromosome origin and turnover. Adv Biotechnol (Singap) 3:17, 2025. Pubmed reference: 40434564. DOI: 10.1007/s44307-025-00068-6.

2021

Ding, W., Zhang, X., Zhao, X., Jing, W., Cao, Z., Li, J., Huang, Y., You, X., Wang, M., Shi, Q., Bing, X. :

A chromosome-level genome assembly of the Mandarin fish (Siniperca chuatsi). Front Genet 12:671650, 2021. Pubmed reference: 34249093. DOI: 10.3389/fgene.2021.671650.

Guo, W., He, S., Liang, X., Tian, C., Dou, Y., Lv, L. :

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs. Anim Genet 52:311-320, 2021. Pubmed reference: 33598959. DOI: 10.1111/age.13046.

Sistrurus catenatus (massasauga) :

2023

Mathur, S., Mason, A.J., Bradburd, G.S., Gibbs, H.L. :

Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Proc Natl Acad Sci U S A 120:e2303043120, 2023. Pubmed reference: 37844221. DOI: 10.1073/pnas.2303043120.

Sminthopsis crassicaudata (fat-tailed dunnart) :

2024

Ibeh, N., Feigin, C.Y., Frankenberg, S.R., McCarthy, D.J., Pask, A.J., Gallego Romero, I. :

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart (Sminthopsis crassicaudata). GigaByte 2024:gigabyte118, 2024. Pubmed reference: 38746537. DOI: 10.46471/gigabyte.118.

Smutsia gigantea (giant pangolin) :

2023

Heighton, S.P., Allio, R., Murienne, J., Salmona, J., Meng, H., Scornavacca, C., Bastos, A.D.S., Njiokou, F., Pietersen, D.W., Tilak, M.K., Luo, S.J., Delsuc, F., Gaubert, P. :

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals. Mol Biol Evol 40:msad190, 2023. Pubmed reference: 37794645. DOI: 10.1093/molbev/msad190.

Somateria mollissima (common eider) :

2024

Tørresen, O.K., Kersten, O., Garmann-Aarhus, B., Helberg, M., Tooming-Klunderud, A., Skage, M., Boessenkool, S., Jakobsen, K.S. :

A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758). J Hered 116:363-372, 2024. Pubmed reference: 39231044. DOI: 10.1093/jhered/esae042.

Sorex fumeus (smoky shrew) :

2024

Cossette, M.L., Stewart, D.T., Shafer, A.B.A. :

Comparative genomics of the world's smallest mammals reveals links to echolocation, metabolism, and body size plasticity. Genome Biol Evol 16:evae225, 2024. Pubmed reference: 39431406. DOI: 10.1093/gbe/evae225.

Sorex maritimensis (Maritime shrew) :

2024

Cossette, M.L., Stewart, D.T., Shafer, A.B.A. :

Sorex ornatus (ornate shrew) :

2025

Linn, I.J., Escalona, M., Nguyen, O., Marimuthu, M.P.A., Chumchim, N., Fairbairn, C.W., Seligmann, W., Beraut, E., Conroy, C.J., Bowie, R.C.K., Nachman, M.W. :

A high-quality reference genome for the ornate shrew (Sorex ornatus). J Hered :esaf074, 2025. Pubmed reference: 41042244. DOI: 10.1093/jhered/esaf074.

Sparidentex hasta (sobaity seabream) :

2022

Karam, Q., Kumar, V., Shajan, A.B., Al-Nuaimi, S., Sattari, Z., El-Dakour, S. :

De-novo genome assembly and annotation of sobaity seabream Sparidentex hasta. Front Genet 13:988488, 2022. Pubmed reference: 36386818. DOI: 10.3389/fgene.2022.988488.

Sparus aurata (gilthead seabream) :

2023

Bertolini, F., Ribani, A., Capoccioni, F., Buttazzoni, L., Bovo, S., Schiavo, G., Caggiano, M., Rothschild, M.F., Fontanesi, L. :

Whole genome sequencing provides information on the genomic architecture and diversity of cultivated gilthead seabream (Sparus aurata) broodstock nuclei. Genes (Basel) 14:839, 2023. Pubmed reference: 37107597. DOI: 10.3390/genes14040839.

Spatula clypeata (Northern shoveler) :

2025

Zhang, Z., Ni, Z., Li, T., Ning, M., Gao, C., Hu, J., Han, M., Yang, J., Wu, F., Chen, L., Lu, L., Wu, Z., Ai, H., Huang, Y. :

Spinibarbus caldwelli :

2025

Fan, Z., Lei, W., Fang, Y., Sheng, J., Zeng, Q., Jian, S., Fang, L., Hong, Y., Zhang, W. :

Chromosome-level genome assembly and annotation of Spinibarbus caldwelli. Sci Data 12:1138, 2025. Pubmed reference: 40610506. DOI: 10.1038/s41597-025-05469-9.

Wu, Y., Li, Y., Cheng, Z., Xu, H., Wang, M., Ye, X., Lai, M., Zhang, D. :

The haplotype-resolved chromosome-level genome assembly of Spinibarbus caldwelli provides insights into environmental adaptability and disease resistance. Comp Biochem Physiol Part D Genomics Proteomics 56:S1744-117X(25)00200-X:101611, 2025. Pubmed reference: 40845583. DOI: 10.1016/j.cbd.2025.101611.

2024

Wu, L., Gu, S., Wen, P., Wu, L., Li, L., Guo, S., Ding, S. :

Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli. Sci Data 11:933, 2024. Pubmed reference: 39198473. DOI: 10.1038/s41597-024-03796-x.

Spondylurus culebrae :

2024

Rivera, D., Henderson, J.B., Lam, A.W., Hostetter, N.J., Collazo, J.A., Bell, R.C. :

High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae. Genome Biol Evol 16:evae079, 2024. Pubmed reference: 38619022. DOI: 10.1093/gbe/evae079.

Spondylurus nitidus :

2024

Rivera, D., Henderson, J.B., Lam, A.W., Hostetter, N.J., Collazo, J.A., Bell, R.C. :

Squaliobarbus curriculus (barbel chub) :

2024

Zheng, Q., Huang, F., Zheng, H., Zhang, H., Wen, R., Li, C. :

Chromosome-level genome assembly and annotation of Barbel chub Squaliobarbus curriculus. Sci Data 11:1453, 2024. Pubmed reference: 39741141. DOI: 10.1038/s41597-024-04354-1.

Squalus acanthias (spiny dogfish) :

2023

Wagner, C.I., Kopp, M.E.L., Thorburn, J., Jones, C.S., Hoarau, G., Noble, L.R. :

Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome. G3 (Bethesda) 13:jkad146, 2023. Pubmed reference: 37395764. DOI: 10.1093/g3journal/jkad146.

Squamata (squamates) :

2025

Colston, T.J., Pirro, S., Pyron, R.A. :

The complete genome sequences of 101 species of reptiles. Biodivers Genomes 2025, 2025. Pubmed reference: 40265171. DOI: 10.56179/001c.129597.

2023

Pinto, B.J., Gamble, T., Smith, C.H., Wilson, M.A. :

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. J Hered 114:445-458, 2023. Pubmed reference: 37018459. DOI: 10.1093/jhered/esad023.

Pinto, B.J., Gamble, T., Smith, C.H., Wilson, M.A. :

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution. bioRxiv , 2023. Pubmed reference: 37034614. DOI: 10.1101/2023.01.20.524006.

Staurois parvus :

2023

Holtz, M.A., Racicot, R., Preininger, D., Stuckert, A.M.M., Mangiamele, L.A. :

Genome assembly of the foot-flagging frog, Staurois parvus: a resource for understanding mechanisms of behavior. G3 (Bethesda) 13:jkad193, 2023. Pubmed reference: 37625789. DOI: 10.1093/g3journal/jkad193.

Steno bredanensis (rough-toothed dolphin) :

2023

Huang, X., Fan, H., Zhou, W., Yang, G., Wei, F. :

The rough-toothed dolphin genome provides new insights into the genetic mechanism of its rough teeth. Integr Zool 18:601-615, 2023. Pubmed reference: 37212019. DOI: 10.1111/1749-4877.12723.

Strigops habroptilus (kakapo) :

2023

Wold, J.R., Guhlin, J.G., Dearden, P.K., Santure, A.W., Steeves, T.E. :

The promise and challenges of characterising genome-wide structural variants: A case study in a critically endangered parrot. Mol Ecol Resour 25:e13783, 2023. Pubmed reference: 36916824. DOI: 10.1111/1755-0998.13783.

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2015

Koepfli, K.P., Paten, B. :

The Genome 10K Project: a way forward. Annu Rev Anim Biosci 3:57-111, 2015. Pubmed reference: 25689317. DOI: 10.1146/annurev-animal-090414-014900.

Strix aluco (tawny owl) :

2024

Baltazar-Soares, M., Karell, P., Wright, D., Nilsson, J.Å., Brommer, J.E. :

Genomic basis of melanin-associated phenotypes suggests colour-specific environmental adaptations in tawny owls. Mol Ecol 33:e17247, 2024. Pubmed reference: 38173194. DOI: 10.1111/mec.17247.

Strix uralensis (Ural owl) :

2025

Winter, S., Meißner, R., Grethlein, M., Wehrenberg, G., Kiebler, A., Silva, A.X., Escobar, N.R., Quesada Calderón, S.M., Suescún, A.V., Belmar, L.G., Prost, S. :

Chromosome-Level genome assembly and transcriptome analysis of the ural owl, Strix uralensis Pallas, 1771. J Hered :esaf038, 2025. Pubmed reference: 40509755. DOI: 10.1093/jhered/esaf038.

Chrysostomakis, I., Mozer, A., Di-Nizo, C.B., Fischer, D., Sargheini, N., von der Mark, L., Huettel, B., Astrin, J.J., Töpfer, T., Böhne, A. :

A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species. Gigascience 14:giaf106, 2025. Pubmed reference: 40986362. DOI: 10.1093/gigascience/giaf106.

Struthio camelus (African ostrich) :

2018

Papoli Yazdi, H., Ellegren, H. :

A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution. Genome Biol Evol 10:2049-2060, 2018. Pubmed reference: 30099482. DOI: 10.1093/gbe/evy163.

Suncus etruscus (white-toothed pygmy shrew) :

2024

Bukhman, Y.V., Meyer, S., Chu, L.F., Abueg, L., Antosiewicz-Bourget, J., Balacco, J., Brecht, M., Dinatale, E., Fedrigo, O., Formenti, G., Fungtammasan, A., Giri, S.J., Hiller, M., Howe, K., Kihara, D., Mamott, D., Mountcastle, J., Pelan, S., Rabbani, K., Sims, Y., Tracey, A., Wood, J.M.D., Jarvis, E.D., Thomson, J.A., Chaisson, M.J.P., Stewart, R. :

Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Sci Data 11:176, 2024. Pubmed reference: 38326333. DOI: 10.1038/s41597-024-03011-x.

Sus scrofa (pig) :

2025

Zhang, Z., Chen, Z., Teng, J., Liu, S., Lin, Q., Wu, J., Gao, Y., Bai, Z. :

FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis. Genomics Proteomics Bioinformatics 23:qzaf006, 2025. Pubmed reference: 39932890. DOI: 10.1093/gpbjnl/qzaf006.

Han, G., Yang, P., Zhang, Y., Li, Q., Fan, X., Chen, R., Yan, C., Zeng, M., Yang, Y., Tang, Z. :

PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies. Genomics Proteomics Bioinformatics 23:qzaf016, 2025. Pubmed reference: 40036767. DOI: 10.1093/gpbjnl/qzaf016.

Chen, L., Tong, X., Wu, Y., Liu, C., Tang, C., Qi, X., Kong, F., Li, M., Jin, L., Zeng, B. :

A dataset of single-cell transcriptomic atlas of Bama pig and potential marker genes across seven tissues. BMC Genom Data 26:16, 2025. Pubmed reference: 40075302. DOI: 10.1186/s12863-025-01308-3.

Veith, A.C., Meudt, J.J., Reichert, J.L., Frank, J.M., Pavelec, D.M., Ladell, B., Speers, J., Zeller, M., Shin, T., Hyman, J.R., Bradfield, C.A., Konsitzke, C.M., Shanmuganayagam, D., Rubinstein, C.D., Berres, M.E. :

The draft genome of the Wisconsin Miniature SwineTM, a valuable biomedical research tool. G3 (Bethesda) 15:jkaf067, 2025. Pubmed reference: 40191916. DOI: 10.1093/g3journal/jkaf067.

Ma, R., Kuang, R., Zhang, J., Sun, J., Xu, Y., Zhou, X., Han, Z., Hu, M., Wang, D., Fu, Y., Zhang, Y., Li, X., Zhu, M., Zhao, S., Xiang, T., Shi, M., Zhao, Y. :

Annotation and assessment of functional variants in livestock through epigenomic data. J Genet Genomics , 2025. Pubmed reference: 40189200. DOI: 10.1016/j.jgg.2025.03.013.

Du, H., Hu, J., Zhang, Z., Wu, Z. :

Chromosome-level genome assembly of the Meishan pig and insights into its domestication mechanisms. Animals (Basel) 15:603, 2025. Pubmed reference: 40003085. DOI: 10.3390/ani15040603.

Zong, W., Chen, L., Zhang, D., Zhang, Y., Wang, J., Hou, X., Chai, J., An, Y., Tian, M., He, X., Song, C., He, J., Liu, X., Wang, L., D'Alessandro, E., Wang, L., Yin, Y., Li, M., Liu, D., Wang, J., Zhang, L. :

Two telomere-to-telomere pig genome assemblies and pan-genome analyses provide insights into genomic structural landscape and genetic adaptations. Imeta 4:e70013, 2025. Pubmed reference: 40236780. DOI: 10.1002/imt2.70013.

Wang, C., Lei, B., Bao, Y., Wang, Z., Chen, C., Zhang, Y., Qin, S., Sun, T., Tang, Z., Liu, Y. :

Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes. iScience 28:112049, 2025. Pubmed reference: 40104067. DOI: 10.1016/j.isci.2025.112049.

Cao, C., Miao, J., Xie, Q., Sun, J., Cheng, H., Zhang, Z., Wu, F., Liu, S., Ye, X., Gong, H., Zhang, Z., Wang, Q., Pan, Y., Wang, Z. :

A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research. Gigascience 14:giaf048, 2025. Pubmed reference: 40372724. DOI: 10.1093/gigascience/giaf048.

The farm animal genotype-tissue expression (FarmGTEx) project. Nat Genet 57:786-796, 2025. Pubmed reference: 40097783. DOI: 10.1038/s41588-025-02121-5.

Kim, S.J., Kang, D., Jang, S., Chai, H.H., Kim, J., Park, W. :

Comprehensive methylomes and transcriptomes of tissue-specific and body-size associated genes in miniature pigs. Gene 965:149658, 2025. Pubmed reference: 40633856. DOI: 10.1016/j.gene.2025.149658.

[No authors listed] :

Correction to: The draft genome of the Wisconsin Miniature SwineTM, a valuable biomedical research tool. G3 (Bethesda) 15:jkaf211, 2025. Pubmed reference: 41026515. DOI: 10.1093/g3journal/jkaf211.

Zhang, W., Zhou, M., Liu, L., Lu, M., Su, S., Wang, C. :

A high-quality chromosome-level genome assembly and annotation of Anqing Six-end-white pig (Sus scrofa). Sci Data 12:1656, 2025. Pubmed reference: 41115900. DOI: 10.1038/s41597-025-05945-2.

Wang, Q., Zhang, Z., Ye, X., Gu, J., Sun, J., Cao, C., Xiao, Q., Chen, Q., Xu, Z., Wang, K., Zhao, W., Sun, H., Zhao, Q., Wang, Q., Pan, Y., Zhang, Z., Wang, Z. :

An updated Pig Haplotype Reference Panel (PHARP 4.0) comprising 13,298 haplotypes. Commun Biol 8:1625, 2025. Pubmed reference: 41266802. DOI: 10.1038/s42003-025-09052-1.

Li, X., Quan, Y., Li, D., Wang, Y., Yuan, T., Cao, M., Wang, J., Ding, R., Wang, S., Shi, X., Zhang, J., Jiang, Y., Derks, M.F.L., Liu, W., Liu, Q., Yu, T. :

PSVRP: a pig structural variant reference panel for complex trait genomics and precision breeding. BMC Genomics 26:1073, 2025. Pubmed reference: 41291430. DOI: 10.1186/s12864-025-12273-7.

2024

Zeng, H., Zhang, W., Lin, Q., Gao, Y., Teng, J., Xu, Z., Cai, X., Zhong, Z., Wu, J., Liu, Y., Diao, S., Wei, C., Gong, W., Pan, X., Li, Z., Huang, X., Chen, X., Du, J. :

PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs. Nucleic Acids Res 52:D980-D989, 2024. Pubmed reference: 37956339. DOI: 10.1093/nar/gkad1080.

Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H. :

A compendium of genetic regulatory effects across pig tissues. Nat Genet 56:112-123, 2024. Pubmed reference: 38177344. DOI: 10.1038/s41588-023-01585-7.

Du, H., Diao, C., Zhuo, Y., Zheng, X., Hu, Z., Lu, S., Jin, W., Zhou, L., Liu, J.F. :

Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity. Genomics 116:S0888-7543(24)00002-8:110782, 2024. Pubmed reference: 38176574. DOI: 10.1016/j.ygeno.2024.110782.

Miao, J., Wei, X., Cao, C., Sun, J., Xu, Y., Zhang, Z., Wang, Q., Pan, Y., Wang, Z. :

Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 15:32, 2024. Pubmed reference: 38389084. DOI: 10.1186/s40104-023-00984-4.

Zong, W., Zhao, R., Wang, X., Zhou, C., Wang, J., Chen, C., Niu, N., Zheng, Y., Chen, L., Liu, X., Hou, X., Zhao, F., Wang, L., Wang, L., Song, C., Zhang, L. :

Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 31:dsae008, 2024. Pubmed reference: 38447059. DOI: 10.1093/dnares/dsae008.

Wang, Y., Gou, Y., Yuan, R., Zou, Q., Zhang, X., Zheng, T., Fei, K., Shi, R., Zhang, M., Li, Y., Gong, Z., Luo, C., Xiong, Y., Shan, D., Wei, C., Shen, L., Tang, G., Li, M., Zhu, L., Li, X., Jiang, Y. :

A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs. Int J Biol Macromol 270:131796, 2024. Pubmed reference: 38677688. DOI: 10.1016/j.ijbiomac.2024.131796.

Yang, L., Yin, H., Bai, L., Yao, W., Tao, T., Zhao, Q., Gao, Y., Teng, J., Xu, Z., Lin, Q., Diao, S., Pan, Z., Guan, D., Li, B., Zhou, H., Zhou, Z., Zhao, F., Wang, Q., Pan, Y., Zhang, Z., Li, K., Fang, L., Liu, G.E. :

Mapping and functional characterization of structural variation in 1060 pig genomes. Genome Biol 25:116, 2024. Pubmed reference: 38715020. DOI: 10.1186/s13059-024-03253-3.

Niu, Y., Fan, X., Yang, Y., Li, J., Lian, J., Wang, L., Zhang, Y., Tang, Y., Tang, Z. :

Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 7:738, 2024. Pubmed reference: 38890535. DOI: 10.1038/s42003-024-06397-x.

Wy, S., Kwon, D., Park, W., Chai, H.H., Cho, I.C., Kim, J. :

A chromosome-level genome assembly of the Korean minipig (Sus scrofa). Sci Data 11:840, 2024. Pubmed reference: 39097649. DOI: 10.1038/s41597-024-03680-8.

Quan, J., Yang, M., Wang, X., Cai, G., Ding, R., Zhuang, Z., Zhou, S., Tan, S., Ruan, D., Wu, J., Zheng, E., Zhang, Z., Liu, L., Meng, F., Wu, J., Xu, C., Qiu, Y., Wang, S., Lin, M., Li, S., Ye, Y., Zhou, F., Lin, D., Li, X., Deng, S., Zhang, Y., Yao, Z., Gao, X., Yang, Y., Liu, Y., Zhan, Y., Liu, Z., Zhang, J., Ma, F., Yang, J., Chen, Q., Yang, J., Ye, J., Dong, L., Gu, T., Huang, S., Xu, Z., Li, Z., Yang, J., Huang, W., Wu, Z. :

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs. Nat Commun 15:5587, 2024. Pubmed reference: 38961076. DOI: 10.1038/s41467-024-49923-5.

Kwon, S.G., Bae, G.H., Hong, J.H., Choi, J.W., Choi, J.H., Lim, N.S., Jeon, C., Mali, N.M., Jun, M.S., Shin, J., Kim, J., Cho, E.S., Han, M.H., Oh, J.W. :

Comprehensive analysis of somatic mutations and structural variations in domestic pig. Mamm Genome 35:645-656, 2024. Pubmed reference: 39177814. DOI: 10.1007/s00335-024-10058-z.

Schwartz, J.C., Farrell, C.P., Freimanis, G., Sewell, A.K., Phillips, J.D., Hammond, J.A. :

A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation. Immunogenetics 76:361-380, 2024. Pubmed reference: 39294478. DOI: 10.1007/s00251-024-01355-7.

Du, H., Lu, S., Huang, Q., Zhou, L., Liu, J.F. :

Chromosome-level genome assembly of Huai pig (Sus scrofa). Sci Data 11:1072, 2024. Pubmed reference: 39358406. DOI: 10.1038/s41597-024-03921-w.

Du, H., Zhuo, Y., Lu, S., Li, W., Zhou, L., Sun, F., Liu, G., Liu, J.F. :

Pangenome reveals gene content variations and structural variants contributing to pig characteristics. Genomics Proteomics Bioinformatics 22:qzae081, 2024. Pubmed reference: 39535885. DOI: 10.1093/gpbjnl/qzae081.

Du, H., Zhou, L., Liu, Z., Zhuo, Y., Zhang, M., Huang, Q., Lu, S., Xing, K., Jiang, L., Liu, J.F. :

The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs. Nat Commun 15:10137, 2024. Pubmed reference: 39578420. DOI: 10.1038/s41467-024-54471-z.

Hu, J., Gui, L., Wu, Z., Huang, L. :

Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression. J Anim Sci Biotechnol 15:162, 2024. Pubmed reference: 39627810. DOI: 10.1186/s40104-024-01121-5.

Chen, H.M., Xu, K.X., Yan, C., Zhao, H., Jiao, D.L., Si, S., Liu, Z.X., Peng, G.Y., Jamal, M.A., Lv, M.J., Wang, P., Zeng, Y.Z., Zhao, H.Y., Wang, M.S., Wei, H.J. :

A chromosome-scale reference genome of the Banna miniature inbred pig. Sci Data 11:1345, 2024. Pubmed reference: 39695204. DOI: 10.1038/s41597-024-04201-3.

Zhang, Y.D., Yuan, W., Bi, H., Yang, X., Zhang, Y.Y., Chen, W. :

Whole-genome resequencing reveals collagen-related genes in Kele pigs. PLoS One 19:e0311417, 2024. Pubmed reference: 39739914. DOI: 10.1371/journal.pone.0311417.

Li, D., Wang, Y., Yuan, T., Cao, M., He, Y., Zhang, L., Li, X., Jiang, Y., Li, K., Sun, J., Lv, G., Su, G., Wang, Q., Pan, Y., Li, X., Jiang, Y., Yang, G., Groenen, M.A.M., Derks, M.F.L., Ding, R., Ding, X., Yu, T. :

Pangenome and genome variation analyses of pigs unveil genomic facets for their adaptation and agronomic characteristics. Imeta 3:e257, 2024. Pubmed reference: 39742300. DOI: 10.1002/imt2.257.

2023

Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., de Magalhães, J.P., Rigden, D.J., Meng, J., Liu, G., Chen, K., Wei, Z. :

Jiang, Y.F., Wang, S., Wang, C.L., Xu, R.H., Wang, W.W., Jiang, Y., Wang, M.S., Jiang, L., Dai, L.H., Wang, J.R., Chu, X.H., Zeng, Y.Q., Fang, L.Z., Wu, D.D., Zhang, Q., Ding, X.D. :

Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 26:106119, 2023. Pubmed reference: 36852268. DOI: 10.1016/j.isci.2023.106119.

Zhang, F., Velez-Irizarry, D., Ernst, C.W., Huang, W. :

Mapping splice QTLs reveals distinct transcriptional and post-transcriptional regulatory variation of gene expression and identifies putative alternative splicing variation mediating complex trait variation in pigs. BMC Genomics 24:240, 2023. Pubmed reference: 37142954. DOI: 10.1186/s12864-023-09314-4.

Ding, R., Savegnago, R., Liu, J., Long, N., Tan, C., Cai, G., Zhuang, Z., Wu, J., Yang, M., Qiu, Y., Ruan, D., Quan, J., Zheng, E., Yang, H., Li, Z., Tan, S., Bedhane, M., Schnabel, R., Steibel, J., Gondro, C., Yang, J., Huang, W., Wu, Z. :

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs. Commun Biol 6:577, 2023. Pubmed reference: 37253973. DOI: 10.1038/s42003-023-04933-9.

Qian, R., Xie, F., Zhang, W., Kong, J., Zhou, X., Wang, C., Li, X. :

Genome-wide detection of CNV regions between Anqing six-end-white and Duroc pigs. Mol Cytogenet 16:12, 2023. Pubmed reference: 37400846. DOI: 10.1186/s13039-023-00646-0.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 34:418-436, 2023. Pubmed reference: 37460664. DOI: 10.1007/s00335-023-10008-1.

Duhan, N., Kaur, S., Kaundal, R. :

Tong, X., Chen, D., Hu, J., Lin, S., Ling, Z., Ai, H., Zhang, Z., Huang, L. :

Accurate haplotype construction and detection of selection signatures enabled by high quality pig genome sequences. Nat Commun 14:5126, 2023. Pubmed reference: 37612277. DOI: 10.1038/s41467-023-40434-3.

Benjamin, N.R., Crooijmans, R.P.M.A., Jordan, L.R., Bolt, C.R., Schook, L.B., Schachtschneider, K.M., Groenen, M.A.M., Roca, A.L. :

Swine global genomic resources: insights into wild and domesticated populations. Mamm Genome 34:520-530, 2023. Pubmed reference: 37805667. DOI: 10.1007/s00335-023-10012-5.

Li, J., Zhao, T., Guan, D., Pan, Z., Bai, Z., Teng, J., Zhang, Z., Zheng, Z., Zeng, J., Zhou, H., Fang, L., Cheng, H. :

Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits. Cell Genom 3:100390, 2023. Pubmed reference: 37868039. DOI: 10.1016/j.xgen.2023.100390.

Li, Z., Liu, X., Wang, C., Li, Z., Jiang, B., Zhang, R., Tong, L., Qu, Y., He, S., Chen, H., Mao, Y., Li, Q., Pook, T., Wu, Y., Zan, Y., Zhang, H., Li, L., Wen, K., Chen, Y. :

The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res 33:1833-1847, 2023. Pubmed reference: 37914227. DOI: 10.1101/gr.277638.122.

Kwon, D., Park, N., Wy, S., Lee, D., Chai, H.H., Cho, I.C., Lee, J., Kwon, K., Kim, H., Moon, Y., Kim, J., Park, W., Kim, J. :

A chromosome-level genome assembly of the Korean crossbred pig Nanchukmacdon (Sus scrofa). Sci Data 10:761, 2023. Pubmed reference: 37923776. DOI: 10.1038/s41597-023-02661-7.

2022

Chen, J., Zhong, J., He, X., Li, X., Ni, P., Safner, T., Šprem, N., Han, J. :

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. Anim Genet 53:281-292, 2022. Pubmed reference: 35238061. DOI: 10.1111/age.13181.

Crespo-Piazuelo, D., Acloque, H., González-Rodríguez, O., Mongellaz, M., Mercat, M.J., Bink, M.C.A.M., Huisman, A.E., Ramayo-Caldas, Y., Sánchez, J.P., Ballester, M. :

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues. Gigascience 12:giad042, 2022. Pubmed reference: 37354463. DOI: 10.1093/gigascience/giad042.

2021

Pan, Z., Yao, Y., Yin, H., Cai, Z., Wang, Y., Bai, L., Kern, C., Halstead, M., Chanthavixay, G., Trakooljul, N., Wimmers, K., Sahana, G., Su, G., Lund, M.S., Fredholm, M., Karlskov-Mortensen, P., Ernst, C.W., Ross, P., Tuggle, C.K., Fang, L., Zhou, H. :

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease. Nat Commun 12:5848, 2021. Pubmed reference: 34615879. DOI: 10.1038/s41467-021-26153-7.

Wang, D., Yang, L., Ning, C., Liu, J.F., Zhao, X. :

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs. BMC Genomics 22:736, 2021. Pubmed reference: 34641784. DOI: 10.1186/s12864-021-08030-1.

Zhang, Y., Fan, G., Liu, X., Skovgaard, K., Sturek, M., Heegaard, P.M.H. :

The genome of the naturally evolved obesity-prone Ossabaw miniature pig. iScience 24:103081, 2021. Pubmed reference: 34585119. DOI: 10.1016/j.isci.2021.103081.

2020

Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Girón, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Schwartz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P.L., Archibald, A.L. :

An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 9:giaa051, 2020. Pubmed reference: 32543654. DOI: 10.1093/gigascience/giaa051.

2018

Keel, B.N., Nonneman, D.J., Lindholm-Perry, A.K., Oliver, W.T., Rohrer, G.A. :

Porcine single nucleotide polymorphisms and their functional effect: an update. BMC Res Notes 11:860, 2018. Pubmed reference: 30514360. DOI: 10.1186/s13104-018-3973-6.

2014

Fernández, A.I., Muñoz, M., Alves, E., Folch, J.M., Noguera, J.L., Enciso, M.P., Rodríguez, M.d.e.l. .C., Silió, L. :

Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 15:148, 2014. Pubmed reference: 25526890. DOI: 10.1186/s12863-014-0148-x.

2012

Freeman, T.C., Ivens, A., Baillie, J.K., Beraldi, D., Barnett, M.W., Dorward, D., Downing, A., Fairbairn, L., Kapetanovic, R., Raza, S., Tomoiu, A., Alberio, R., Wu, C., Su, A.I., Summers, K.M., Tuggle, C.K., Archibald, A.L., Hume, D.A. :

A gene expression atlas of the domestic pig. BMC Biol 10:90, 2012. Pubmed reference: 23153189. DOI: 10.1186/1741-7007-10-90.

Tortereau, F., Servin, B., Frantz, L., Megens, H.J., Milan, D., Rohrer, G., Wiedmann, R., Beever, J., Archibald, A.L., Schook, L.B., Groenen, M.A. :

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics 13:586, 2012. Pubmed reference: 23152986. DOI: 10.1186/1471-2164-13-586.

Groenen, M.A., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.L., Humphray, S.J., Hunt, T., Hornshøj, H., Jeon, J.T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.H., Kim, K.W., Kim, T.H., Larson, G., Lee, K., Lee, K.T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Nguyen, D.T., Ni, P., Oh, S.J., Onteru, S., Panitz, F., Park, E.W., Park, H.S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., Schook, L.B. :

Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-8, 2012. Pubmed reference: 23151582. DOI: 10.1038/nature11622.

2010

Archibald, A.L., Bolund, L., Churcher, C., Fredholm, M., Groenen, M.A., Harlizius, B., Lee, K.T., Milan, D., Rogers, J., Rothschild, M.F., Uenishi, H., Wang, J., Schook, L.B. :

Pig genome sequence--analysis and publication strategy. BMC Genomics 11:438, 2010. Pubmed reference: 20642822. DOI: 10.1186/1471-2164-11-438.

2009

Ramos, A.M., Crooijmans, R.P., Affara, N.A., Amaral, A.J., Archibald, A.L., Beever, J.E., Bendixen, C., Churcher, C., Clark, R., Dehais, P., Hansen, M.S., Hedegaard, J., Hu, Z.L., Kerstens, H.H., Law, A.S., Megens, H.J., Milan, D., Nonneman, D.J., Rohrer, G.A., Rothschild, M.F., Smith, T.P., Schnabel, R.D., Van Tassell, C.P., Taylor, J.F., Wiedmann, R.T., Schook, L.B., Groenen, M.A. :

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4:e6524, 2009. Pubmed reference: 19654876. DOI: 10.1371/journal.pone.0006524.

Amaral, A.J., Megens, H.J., Kerstens, H.H., Heuven, H.C., Dibbits, B., Crooijmans, R.P., den Dunnen, J.T., Groenen, M.A. :

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 10:374, 2009. Pubmed reference: 19674453. DOI: 10.1186/1471-2164-10-374.

2007

Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Yang, F., Rogatcheva, M.B., Milan, D., Chardon, P., Rohrer, G., Nonneman, D., de Jong, P., Meyers, S.N., Archibald, A., Beever, J.E., Schook, L.B., Rogers, J. :

A high utility integrated map of the pig genome. Genome Biol 8:R139, 2007. Pubmed reference: 17625002. DOI: 10.1186/gb-2007-8-7-r139.

2005

Schook, L.B., Beever, J.E., Rogers, J., Humphray, S., Archibald, A., Chardon, P., Milan, D., Rohrer, G., Eversole, K. :

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp Funct Genomics 6:251-5, 2005. Pubmed reference: 18629187. DOI: 10.1002/cfg.479.

2003

Karsenty, E., Barillot, E., Tosser-Klopp, G., Lahbib-Mansais, Y., Milan, D., Hatey, F., Cirera, S., Sawera, M., Jorgensen, C.B., Chowdhary, B., Fredholm, M., Wimmers, K., Ponsuksili, S., Davoli, R., Fontanesi, L., Braglia, S., Zambonelli, P., Bigi, D., Neuenschwander, S., Gellin, J. :

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa) Nucleic Acids Research 31:138-41, 2003. Pubmed reference: 12519967.

Martins-Wess, F., Milan, D., Drogemuller, C., Vobeta-Nemitz, R., Brenig, B., Robic, A., Yerle, M., Leeb, T. :

A high resolution physical and RH map of pig chromosome 6q1.2 and comparative analysis with human chromosome 19q13.1 BMC Genomics 4:20, 2003. Pubmed reference: 12744726. DOI: 10.1186/1471-2164-4-20.

Rothschild, M.F. :

From a sow's ear to a silk purse: real progress in porcine genomics. Cytogenet Genome Res 102:95-9, 2003. Pubmed reference: 14970686. DOI: 75732.

2002

Jiang, Z.H., Melville, J.S., Cao, H.H., Kumar, S., Filipski, A., Gibbins, A.M.V. :

Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome Genome 45:769-776, 2002. Pubmed reference: 12175081.

Yerle, M., Pinton, P., Delcros, C., Arnal, N., Milan, D., Robic, A. :

Generation and characterization of a 12,,000-rad radiation hybrid panel for fine mapping in pig Cytogenetic & Genome Research 97:219-228, 2002.

Rink, A., Santschi, E.M., Eyer, K.M., Roelofs, B., Hess, M., Godfrey, M., Karajusuf, E.K., Yerle, M., Milan, D., Beattie, C.W. :

A first-generation EST RH comparative map of the porcine and human genome Mammalian Genome 13:578-87, 2002. Pubmed reference: 12420136. DOI: 10.1007/s00335-002-2192-5.

1999

Hawken, R.J., Murtaugh, J., Flickinger, G.H., Yerle, M., Robic, A., Milan, D., Gellin, J., Beattie, C.W., Schook, L.B., Alexander, L.J. :

A first-generation porcine whole-genome radiation hybrid map Mammalian Genome 10:824-830, 1999. Pubmed reference: 10430669.

Mikawa, S., Akita, T., Hisamatsu, N., Inage, Y., Ito, Y., Kobayashi, E., Kusumoto, H., Matsumoto, T., Mikami, H., Minezawa, M., Miyake, M., Shimanuki, S., Sugiyama, C., Uchida, Y., Wada, Y., Yanai, S., Yasue, H. :

A linkage map of 243 DNA markers in an intercross of Gottingen miniature and Meishan pigs Animal Genetics 30:407-417, 1999. Pubmed reference: 10612229.

1998

Yerle, M., Pinton, P., Robic, A., Alfonso, A., Palvadeau, Y., Delcros, C., Hawken, R., Alexander, L., Beattie, C., Schook, L., Milan, D., Gellin, J. :

Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs Cytogenetics & Cell Genetics 82:182-188, 1998.

1997

Ambady, S., Mendiola, J.R., Louis, C.F., Janzen, M.A., Schook, L.B., Buoen, L., Lunney, J.K., Grimm, D.R., Deleon, F.A.P. :

Development and use of a microdissected swine chromosome 6 dna library Cytogenetics & Cell Genetics 76:27-33, 1997.

Rohrer, G.A., Alexander, L.J., Beattie, C.W., Wilkie, P., Flickinger, G.H., Schook, L.B., Paszek, A.A., Andersson, L., Mariani, P., Marklund, L., Fredholm, M., Hoyheim, B., Archibald, A.L., Nielsen, V.H., Milan, D., Groenen, M.A.M. :

A consensus linkage map for swine chromosome 7 Animal Genetics 28:223-229, 1997.

Yerle, M., Lahbibmansais, Y., Pinton, P., Robic, A., Goureau, A., Milan, D., Gellin, J. :

The cytogenetic map of the domestic pig (sus scrofa domestica) [Review] Mammalian Genome 8:592-607, 1997. Pubmed reference: 9250869.

Andersson, L. :

The use of a wild pig x domestic pig intercross to map phenotypic trait loci J Hered 88:380-3, 1997. Pubmed reference: 9378913. DOI: 10.1093/oxfordjournals.jhered.a023122.

1996

Fronicke, L., Chowdhary, B.P., Scherthan, H., Gustavsson, I. :

A comparative map of the porcine and human genomes demonstrates zoo-FISH and gene mapping-based chromosomal homologies Mammalian Genome 7:285-290, 1996. Pubmed reference: 8661700.

Rohrer, G.A., Alexander, L.J., Hu, Z.L., Smith, T.P.L., Keele, J.W., Beattie, C.W. :

A comprehensive map of the porcine genome Genome Research 6:371-391, 1996. Pubmed reference: 8743988.

Marklund, L., Johansson Moller, M., Høyheim, B., Davies, W., Fredholm, M., Juneja, R.K., Mariani, P., Coppieters, W., Ellegren, H., Andersson, L. :

A comprehensive linkage map of the pig based on a wild pig-Large White intercross. Anim Genet 27:255-69, 1996. Pubmed reference: 8856923. DOI: 10.1111/j.1365-2052.1996.tb00487.x.

Rettenberger, G., Bruch, J., Hameister, H. :

A comparative mapping approach to the pig genome Journal of Animal Breeding & Genetics-Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 113:331-338, 1996.

Comparative genome organization of vertebrates Mammalian Genome 7:717-734, 1996. Pubmed reference: 8854859.

Goureau, A., Yerle, M., Schmitz, A., Riquet, J., Milan, D., Pinton, P., Frelat, G., Gellin, J. :

Human and porcine correspondence of chromosome segments using bidirectional chromosome painting. Genomics 36:252-62, 1996. Pubmed reference: 8812451. DOI: 10.1006/geno.1996.0460.

Bosma, A.A., de Haan, N.A., Mellink, C.H., Yerle, M., Zijlstra, C. :

Chromosome homology between the domestic pig and the babirusa (family Suidae) elucidated with the use of porcine painting probes. Cytogenet Cell Genet 75:32-5, 1996. Pubmed reference: 8995485. DOI: 10.1159/000134452.

Sarkhel, B.C., Tyagi, B., Parekh, H.K.B. :

Chromosome profile of desi pigs (sus scrofa domesticus). Indian Journal of Animal Sciences 66:405-407, 1996.

1995

Archibald, A.L., Haley, C.S., Brown, J.F., Couperwhite, S., McQueen, H.A., Nicholson, D., Coppieters, W., Weghe, A. van de, Stratil, A., Wintero, A.K., Fredholm, M., Larsen, N.J., Nielsen, V.H., Milan, D., Woloszyn, N., Robic, A., Dalens, M., Riquet, J., Gellin, J., Caritez, J.C., Burgaud, G., Ollivier, L., Bidanel, J.P., Vaiman, M., Renard, C., Geldermann, H., Davoli, R., Ruyter, D., Verstege, E.J.M., Groenen, M.A.M., Davies, W., Hoyheim, B., Keiserud, A., Andersson, L., Ellegren, H., Johansson, M., Marklund, L., Miller, J.R., Dear, D.V.A., Signer, E., Jeffreys, A.J., Moran, C., Le Tissier, P., Muladno, Rothschild, M.F., Tuggle, C.K., Vaske, D., Helm, J., Liu, H.-C., Rahman, A., Yu, T.-P., Larson, R.G., Schmitz, C.B. :

The PiGMaP consortium linkage map of the pig (Sus scrofa) Mammalian Genome 6:157-175, 1995. Pubmed reference: 7749223.

Yerle, M., Lahbibmansais, Y., Mellink, C., Goureau, A., Pinton, P., Echard, G., Gellin, J., Zijlstra, C., Dehaan, N., Bosma, A.A., Chowdhary, B., Gu, F., Gustavsson, I., Thomsen, P.D., Christensen, K., Rettenberger, G., Hameister, H., Schmitz, A., Chaput, B., Frelat, G. :

The PiGMaP consortium cytogenetic map of the domestic pig (Sus scrofa domestica) Mammalian Genome 6:176-186, 1995. Pubmed reference: 7749224.

Rettenberger, G., Klett, C., Zechner, U., Kunz, J., Vogel, W., Hameister, H. :

Visualization of the conservation of synteny between humans and pigs by heterologous chromosomal painting Genomics 26:372-378, 1995. Pubmed reference: 7601464.

Ollivier, L. :

Genetic differences in recombination frequency in the pig (sus scrofa) Genome 38:1048-1051, 1995. Pubmed reference: 8536996.

Rønne, M. :

Localization of landmarks and bands in the karotype of Sus scrofa domestica. Comparison between different classifications. Hereditas 123:155-68, 1995. Pubmed reference: 8984097. DOI: 10.1111/j.1601-5223.1995.00155.x.

Panda, A.K., Chatterje, A.K., Sahoo, A.K., Roy, S., Samanta, S. :

Chromosome study on a wild boar from sunderban tiger reserve. Indian Journal of Animal Sciences 65:1272-1274, 1995.

Graphodatsky, A.S., Biltueva, L.S. :

Chromosome banding and gene conservation between humans and pigs. Journal of Animal Breeding and Genetics - Zeitschrift Fur Tierzuchtung und Zuchtungsbiologie 112:151-155, 1995.

Palegar, M.S., Govindaiaii, M.G., Nagaraja, C.S., Jayashankar, M.R. :

Chromosomal studies on exotic and local non-descriptive pigs. Indian Journal of Animal Sciences 65:799-800, 1995.

1994

Rohrer, G.A., Alexander, L.J., Keele, J.W., Smith, T.P., Beattie, C.W. :

A Microsatellite Linkage Map of the Porcine Genome Genetics 136:231-245, 1994. Pubmed reference: 8138161.

Ellegren, H., Chowdhary, B.P., Johansson, M., Marklund, L., Fredholm, M., Gustavsson, I., Andersson, L. :

A primary linkage map of the porcine genome reveals a low rate of genetic recombination Genetics 137:1089-1100, 1994. Pubmed reference: 7982563.

Beattie, C.W. :

Livestock genome maps Trends in Genetics 10:334-338, 1994. Pubmed reference: 7974748.

1993

Langford, C.F., Telenius, H., Miller, N.G., Thomsen, P.D., Tucker, E.M. :

Preparation of chromosome-specific paints and complete assignment of chromosomes in the pig flow karyotype. Anim Genet 24:261-7, 1993. Pubmed reference: 8239070. DOI: 10.1111/j.1365-2052.1993.tb00309.x.

Villagómez, D.A. :

Zygotene-pachytene substaging and synaptonemal complex karyotyping of boar spermatocytes. Hereditas 118:87-99, 1993. Pubmed reference: 8478210. DOI: 10.1111/j.1601-5223.1993.t01-3-00087.x.

Yerle, M., Schmitz, A., Milan, D., Chaput, B., Monteagudo, L., Vaiman, M., Frelat, G., Gellin, J. :

Accurate characterization of porcine bivariate flow karyotype by PCR and fluorescence in situ hybridization. Genomics 16:97-103, 1993. Pubmed reference: 8486390. DOI: 10.1006/geno.1993.1146.

Daniel, H., Thiagarajan, V., Kandasamy, N. :

Karyotype Analysis of G-Band Chromosomes of Desi Pigs, Large White Yorkshire and Their Crosses. Indian Veterinary Journal 70:531-535, 1993.

Rao, K.B.C.A., Bhat, P.P., Bhat, P.N. :

Chromosome Banding Patterns of Indian Domestic Pig. Indian Journal of Animal Sciences 63:849-856, 1993.

1992

Echard, G., Milan, D., Yerle, M., Lahbibmansais, Y., Gellin, J. :

The Gene Map of the Pig (Sus-Scrofa-Domestica L) - A Review Cytogenetics and Cell Genetics 61:146-151, 1992. Pubmed reference: 1395726.

Schmitz, A., Chardon, P., Gainche, I., Chaput, B., Guilly, M.N., Frelat, G., Vaiman, M. :

Pig standard bivariate flow karyotype and peak assignment for chromosomes X, Y, 3, and 7. Genomics 14:357-62, 1992. Pubmed reference: 1427852. DOI: 10.1016/s0888-7543(05)80226-5.

Daniel, H., Thiagarajan, V., Kandasamy, N. :

An Improved Leucocyte Culture Technique for Display of Porcine Chromosomes. Indian Veterinary Journal 69:756-757, 1992.

1991

Poulsen, B.S., Kristiansen, K., Rønne, M. :

Comparative analysis of autosomes in karyotypes from pig and rabbit using RBG-banding and in situ hybridization. Cytobios 67:23-7, 1991. Pubmed reference: 1935256.

Yerle, M., Galman, O., Echard, G. :

The high-resolution GTG-banding pattern of pig chromosomes. Cytogenet Cell Genet 56:45-7, 1991. Pubmed reference: 2004556. DOI: 10.1159/000133044.

Galman, O., Yerle, M., Echard, G. :

The High-Resolution G- Banded Karyotype of Sus-Scrofa- Domestica-L. Genetics Selection Evolution 23:S113-S116, 1991.

Vijh, R.K., Sahai, R., Sharma, A. :

G-Banded Chromosomal Profile of Indian Domestic Pig. Indian Journal of Animal Sciences 61:324-327, 1991.

1990

Bhagirath, T. :

C-band fusion and behaviour of the involved chromosomes during meiotic prophase I of the male domestic pig. Hereditas 112:265-70, 1990. Pubmed reference: 2211180. DOI: 10.1111/j.1601-5223.1990.tb00065.x.

Nombela, J.J.A., Murcia, C.R., Abaigar, T., Vericad, J.R. :

Cytogenetic Analysis (Gtg, CBG and Nor Bands) of a Wild Boar Population (Sus-Scrofa-Scrofa) with Chromosomal Polymorphism in the South-East of Spain. Genetics Selection Evolution 22:1-9, 1990.

Vijh, R.K., Sahai, R., Sharma, A. :

Chromosomal Profile of Indian Domestic Pig. Indian Journal of Animal Sciences 60:1373-1376, 1990.

1989

Popescu, C.P., Boscher, J., Malynicz, G.L. :

Chromosome R-banding patterns and NOR homologies in the European wild pig and four breeds of domestic pig. Ann Genet 32:136-40, 1989. Pubmed reference: 2817772.

1988

Gustavsson, I. :

Standard karyotype of the domestic pig. Committee for the Standardized Karyotype of the Domestic Pig. Hereditas 109:151-7, 1988. Pubmed reference: 3230021. DOI: 10.1111/j.1601-5223.1988.tb00351.x.

1987

Rønne, M., Poulsen, B.S., Shibasaki, Y., Flou, S., Elberg, J.J. :

The high resolution R-banded karyotype of the domestic pig, Sus scrofa domestica L. Cytobios 49:103-9, 1987. Pubmed reference: 3568755.

Creighton, P., Houghton, J.A. :

Visualization of pig sperm chromosomes by in-vitro penetration of zona-free hamster ova. J Reprod Fertil 80:619-22, 1987. Pubmed reference: 3656289. DOI: 10.1530/jrf.0.0800619.

1986

Boer, P. de., Hoeven, F.A. van der., Cuijpers, M.P. :

Genetic constitution of early stage pig embryos and embryo mortality. Embryonic mortality in farm animals. Martinus Nijhoff, Dordrecht, Netherlands :207-215, 1986.

1982

Long, S.E., Williams, C.V. :

A comparison of the chromosome complement of inner cell mass and trophoblast cells in day-10 pig embryos. J Reprod Fertil 66:645-8, 1982. Pubmed reference: 7175818. DOI: 10.1530/jrf.0.0660645.

Popescu, C., Lauvergne, J., Malynicz, G. :

[Not Available]. Ann Genet Sel Anim 14:237-40, 1982. Pubmed reference: 22896234. DOI: 10.1186/1297-9686-14-2-237.

Gutierrez, C., Sanchez, A., Betancourt, A. :

[C-band studies of centromeric heterochromatin in pigs (Sus scrofa)]. Revista de Salud Animal 4:119-128, 1982.

Zeng, Y., Luo, L., Cao, X., Shan, X., Chen, Y. :

[Karyotype studies of domestic pigs in southern China]. Acta Veterinaria et Zootechnica Sinica 13:167-172, 1982.

1980

Ford, C.E., Pollock, D.L., Gustavsson, I. :

1972

Hansen-Melander, E., Melander, Y. :

A malformed pig with a normal female karyotype. Hereditas 70:154, 1972. Pubmed reference: 4680632. DOI: 10.1111/j.1601-5223.1972.tb01004.x.

1968

Rary, J.M., Henry, V.G., Matschke, G.H., Murphree, R.L. :

The cytogenetics of swine in the Tellico Wildlife Management Area of Tennessee. Journal of Heredity 59:201-204, 1968.

1964

Cerny, L., Jurmanova, K. :

Somatic chromosomes in swine. Sbornik Vysoke Skoly Zemedelske Brne, Series B 12:307-309, 1964.

None

[No authors listed] :

J Genet Genomics 51:394-406, None. Pubmed reference: 38056526. DOI: 10.1016/j.jgg.2023.11.005.

Sylvia atricapilla (blackcap) :

2023

Bours, A., Pruisscher, P., Bascón-Cardozo, K., Odenthal-Hesse, L., Liedvogel, M. :

The blackcap (Sylvia atricapilla) genome reveals a recent accumulation of LTR retrotransposons. Sci Rep 13:16471, 2023. Pubmed reference: 37777595. DOI: 10.1038/s41598-023-43090-1.

Sylvicapra grimmia (bush duiker) :

1996

Robinson, T.J., Wilson, V., Gallagher, D.S., Taylor, J.F., Davis, S.K., Harrison, W.R., Elder, F.F. :

Symphalangus syndactylus (siamang) :

2025

Complete sequencing of ape genomes. Nature 641:401-418, 2025. Pubmed reference: 40205052. DOI: 10.1038/s41586-025-08816-3.

2024

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G.A., Solar, S.J., Antipov, D., Pickett, B.D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J.M., Lin, J., Sequeira, A.N., Mangan, R.J., Hickey, G., Anez, G.M., Balachandran, P., Bankevich, A., Beck, C.R., Biddanda, A., Borchers, M., Bouffard, G.G., Brannan, E., Brooks, S.Y., Carbone, L., Carrel, L., Chan, A.P., Crawford, J., Diekhans, M., Engelbrecht, E., Feschotte, C., Formenti, G., Garcia, G.H., de Gennaro, L., Gilbert, D., Green, R.E., Guarracino, A., Gupta, I., Haddad, D., Han, J., Harris, R.S., Hartley, G.A., Harvey, W.T., Hiller, M., Hoekzema, K., Houck, M.L., Jeong, H., Kamali, K., Kellis, M., Kille, B., Lee, C., Lee, Y., Lees, W., Lewis, A.P., Li, Q., Loftus, M., Loh, Y.H.E., Loucks, H., Ma, J., Mao, Y., Martinez, J.F.I., Masterson, P., McCoy, R.C., McGrath, B., McKinney, S., Meyer, B.S., Miga, K.H., Mohanty, S.K., Munson, K.M., Pal, K., Pennell, M., Pevzner, P.A., Porubsky, D., Potapova, T., Ringeling, F.R., Rocha, J.L., Ryder, O.A., Sacco, S., Saha, S., Sasaki, T., Schatz, M.C., Schork, N.J., Shanks, C., Smeds, L., Son, D.R., Steiner, C., Sweeten, A.P., Tassia, M.G., Thibaud-Nissen, F., Torres-González, E., Trivedi, M., Wei, W., Wertz, J., Yang, M., Zhang, P., Zhang, S., Zhang, Y., Zhang, Z., Zhao, S.A., Zhu, Y., Jarvis, E.D., Gerton, J.L., Rivas-González, I., Paten, B., Szpiech, Z.A., Huber, C.D., Lenz, T.L., Konkel, M.K., Yi, S.V., Canzar, S., Watson, C.T., Sudmant, P.H., Molloy, E., Garrison, E., Lowe, C.B., Ventura, M., O'Neill, R.J., Koren, S., Makova, K.D., Phillippy, A.M., Eichler, E.E. :

Complete sequencing of ape genomes. bioRxiv , 2024. Pubmed reference: 39131277. DOI: 10.1101/2024.07.31.605654.

Syncerus caffer (African buffalo) :

2024

Talenti, A., Wilkinson, T., Cook, E.A., Hemmink, J.D., Paxton, E., Mutinda, M., Ngulu, S.D., Jayaraman, S., Bishop, R.P., Obara, I., Hourlier, T., Garcia Giron, C., Martin, F.J., Labuschagne, M., Atimnedi, P., Nanteza, A., Keyyu, J.D., Mramba, F., Caron, A., Cornelis, D., Chardonnet, P., Fyumagwa, R., Lembo, T., Auty, H.K., Michaux, J., Smitz, N., Toye, P., Robert, C., Prendergast, J.G.D., Morrison, L.J. :

Continent-wide genomic analysis of the African buffalo (Syncerus caffer). Commun Biol 7:792, 2024. Pubmed reference: 38951693. DOI: 10.1038/s42003-024-06481-2.

Syngnathus scovelli (Gulf pipefish) :

2023

Ramesh, B., Small, C.M., Healey, H., Johnson, B., Barker, E., Currey, M., Bassham, S., Myers, M., Cresko, W.A., Jones, A.G. :

Improvements to the Gulf pipefish Syngnathus scovelli genome. GigaByte 2023:gigabyte76, 2023. Pubmed reference: 36969711. DOI: 10.46471/gigabyte.76.

Tachyglossus aculeatus (Australian echidna) :

2025

Zhou, Y., Jin, J., Li, X., Gedman, G., Pelan, S., Rhie, A., Jiang, C., Fedrigo, O., Howe, K., Phillippy, A.M., Jarvis, E.D., Grutzner, F., Zhou, Q., Zhang, G. :

Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes. Gigascience 14:giae112, 2025. Pubmed reference: 39778707. DOI: 10.1093/gigascience/giae112.

2021

Platypus and echidna genomes reveal mammalian biology and evolution. Nature 592:756-762, 2021. Pubmed reference: 33408411. DOI: 10.1038/s41586-020-03039-0.

Tachysurus fulvidraco x Tachysurus vachelli (hybrid yellow catfish) :

2021

Zhou, H., Duan, G., Jiang, H., Ling, J., Hu, Y., Zhang, Y., Wang, H., Pan, T., Chen, X. :

High-density genetic map and QTL mapping for body color of the yellow catfish (Tachysurus fulvidraco♀ × T. vachellii♂). Anim Genet 52:246-248, 2021. Pubmed reference: 33503316. DOI: 10.1111/age.13042.

Tachysurus vachellii :

2025

Liu, H., Zhang, J., Cui, T., Zhang, X., Li, K., Wang, F., Luo, Q., Fei, S., Chen, B., Zhu, C., Chen, K., Zhu, X., Li, B., Zhao, J., Fang, L., Ou, M. :

A chromosome-level genome assembly of the male darkbarbel catfish (Pelteobagrus vachelli) using PacBio HiFi and Hi-C data. Sci Data 12:351, 2025. Pubmed reference: 40016230. DOI: 10.1038/s41597-025-04662-0.

Liu, H., Zhang, J., Cui, T., Zhang, X., Li, K., Wang, F., Luo, Q., Fei, S., Chen, B., Zhu, C., Chen, K., Zhu, X., Li, B., Zhao, J., Fang, L., Ou, M. :

Publisher Correction: A chromosome-level genome assembly of the male darkbarbel catfish (Pelteobagrus vachelli) using PacBio HiFi and Hi-C data. Sci Data 12:470, 2025. Pubmed reference: 40113785. DOI: 10.1038/s41597-025-04795-2.

2023

Gong, G., Ke, W., Liao, Q., Xiong, Y., Hu, J., Mei, J. :

A chromosome-level genome assembly of the darkbarbel catfish Pelteobagrus vachelli. Sci Data 10:598, 2023. Pubmed reference: 37684295. DOI: 10.1038/s41597-023-02509-0.

Taeniopygia guttata (zebra finch) :

2021

Towards complete and error-free genome assemblies of all vertebrate species. Nature 592:737-746, 2021. Pubmed reference: 33911273. DOI: 10.1038/s41586-021-03451-0.

2008

Stapley, J., Birkhead, TR., Burke, T., Slate, J. :

A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 179:651-67, 2008. Pubmed reference: 10506561.

Takifugu :

2025

He, R.S., Zhao, R., Lin, J.J., Li, Y., Kong, X.Z., Xu, J.X., Wu, J.H., Bu, X.J., Zhang, Y.J., Sun, Y. :

Construction of the graph genomes of Takifugu provides novel insights into the genomic mechanisms of population structure and migratory traits. BMC Biol 23:195, 2025. Pubmed reference: 40598134. DOI: 10.1186/s12915-025-02296-7.

Tanypteryx hageni :

2023

Tolman, E.R., Beatty, C.D., Bush, J., Kohli, M., Moreno, C.M., Ware, J.L., Webber, K.S., Khan, R., Maheshwari, C., Weisz, D., Dudchenko, O., Aiden, E.L., Frandsen, P.B. :

A chromosome-length assembly of the black petaltail (Tanypteryx hageni) dragonfly. Genome Biol Evol 15:evad024, 2023. Pubmed reference: 36807678. DOI: 10.1093/gbe/evad024.

Tapirus indicus (Asiatic tapir) :

2008

Tautogolabrus adspersus (cunner) :

2023

Nugent, C.M., Kess, T., Brachmann, M.K., Langille, B.L., Duffy, S.J., Lehnert, S.J., Wringe, B.F., Bentzen, P., Bradbury, I.R. :

Whole-genome sequencing reveals fine-scale environment-associated divergence near the range limits of a temperate reef fish. Mol Ecol 32:4742-4762, 2023. Pubmed reference: 37430462. DOI: 10.1111/mec.17063.

Teratoscincus roborowskii :

2025

Yang, P., Wei, C., Chang, H., Li, X., Wang, J. :

Chromosome-level genome assembly of Turpan wonder gecko (Teratoscincus roborowskii) reveals olfactory candidate genes. Sci Data 12:1682, 2025. Pubmed reference: 41131014. DOI: 10.1038/s41597-025-05969-8.

Testudines (turtles) :

2025

Colston, T.J., Pirro, S., Pyron, R.A. :

The complete genome sequences of 101 species of reptiles. Biodivers Genomes 2025, 2025. Pubmed reference: 40265171. DOI: 10.56179/001c.129597.

Testudo graeca (Mediterranean spur-thighed tortoise) :

2024

Mira-Jover, A., Graciá, E., Giménez, A., Fritz, U., Rodríguez-Caro, R.C., Bourgeois, Y. :

Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca. PLoS One 19:e0303408, 2024. Pubmed reference: 39121089. DOI: 10.1371/journal.pone.0303408.

Thomomys bottae (Botta's pocket gopher) :

2024

Voss, E.R., Escalona, M., Kozak, K.M., Seligmann, W., Fairbairn, C.W., Nguyen, O., Marimuthu, M.P.A., Conroy, C.J., Patton, J.L., Bowie, R.C.K., Nachman, M.W. :

De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae). J Hered 116:513-523, 2024. Pubmed reference: 39188078. DOI: 10.1093/jhered/esae045.

Thunnus albacares (yellowfin tuna) :

2024

Dimens, P.V., Jones, K.L., Margulies, D., Scholey, V., Cusatti, S., McPeak, B., Hildahl, T.E., Saillant, E.A.E. :

Genomic resources for the Yellowfin tuna Thunnus albacares. Mol Biol Rep 51:232, 2024. Pubmed reference: 38281308. DOI: 10.1007/s11033-023-09117-6.

Thymallus thymallus (grayling) :

2019

Sävilammi, T., Primmer, C.R., Varadharajan, S., Guyomard, R., Guiguen, Y., Sandve, S.R., Vøllestad, L.A., Papakostas, S., Lien, S. :

The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (Bethesda) 9:1283-1294, 2019. Pubmed reference: 30833292. DOI: 10.1534/g3.118.200919.

Thyrsites atun (snoek) :

2023

Mthethwa, S., Bester-van der Merwe, A., Roodt-Wilding, R. :

The complete mitochondrial genome of the South African snoek Thyrsites atun (Euphrasén, 1791) (Perciformes, Gempylidae). Mitochondrial DNA B Resour 8:288-291, 2023. Pubmed reference: 36845005. DOI: 10.1080/23802359.2023.2179353.

Tiaroga cobitis (loach minnow) :

2023

Alexandre, N.M., Cameron, A.C., Tian, D., Chatla, K., Kolora, S.R.R., Whiteman, N.K., Turner, T.F., Reinthal, P.N. :

Trachidermus fasciatus (roughskin sculpin) :

2025

Liu, T., Huang, K., Xu, A., Lü, Z., Gong, L., Liu, J., Tang, M., Liu, L. :

Genome sequencing provides novel insights into diadromous migration adaptations in the roughskin sculpin, Trachidermus fasciatus (Scorpaeniformes, Cottidae). Zookeys 1256:293-316, 2025. Pubmed reference: 41179239. DOI: 10.3897/zookeys.1256.153772.

Trachinotus anak (oyster pompano) :

2025

Wang, T., Guo, Y., Wang, Y., Chen, R., Ge, S., Chen, H. :

Telomere-to-telomere haplotype-resolved genome assembly of a female oyster pompano (Trachinotus anak). Sci Data , 2025. Pubmed reference: 41330948. DOI: 10.1038/s41597-025-06345-2.

Trachinotus ovatus (derbio) :

2023

Luo, H., Zhang, Y., Liu, F., Zhao, Y., Peng, J., Xu, Y., Chen, X., Huang, Y., Ji, C., Liu, Q., He, P., Feng, P., Yang, C., Wei, P., Ma, Z., Qin, J., Zhou, S., Dai, S., Zhang, Y., Zhao, Z., Liu, H., Zheng, H., Zhang, J., Lin, Y., Chen, X. :

The male and female genomes of golden pompano (Trachinotus ovatus) provide insights into the sex chromosome evolution and rapid growth. J Adv Res 65:1-17, 2023. Pubmed reference: 38043610. DOI: 10.1016/j.jare.2023.11.030.

Trachurus trachurus (Atlantic horse mackerel) :

2022

Genner, M., Collins, R. :

The genome sequence of the Atlantic horse mackerel, Trachurus trachurus (Linnaeus 1758). Wellcome Open Res 7:118, 2022. Pubmed reference: 36874570. DOI: 10.12688/wellcomeopenres.17813.1.

Trachypithecus francoisi (Francois's langur) :

2025

Zhijin, L., Zhang, X., Wang, P., Hong, M., Yan, X., Qi, X., Zhao, Q., Chen, Z., Nie, H., Li, H., Li, Z., Zhang, L., Qi, J., He, C., Van Truong, N., Le, M.D., Nadler, T., Imai, H., Roos, C., Li, M. :

Living on the rocks: Genomic analysis of limestone langurs provides novel insights into the adaptive evolution in extreme karst environments. Genomics Proteomics Bioinformatics 23:qzaf007, 2025. Pubmed reference: 39932879. DOI: 10.1093/gpbjnl/qzaf007.

Tragelaphus eurycerus (bongo) :

2025

Holm, K.M., Koepfli, K.P., Pukazhenthi, B.S., Ratan, A., Fryxell, K.J., Pham, M., Weisz, D., Dudchenko, O., Aiden, E.L., Lim, H.C. :

Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): A resource for conservation and comparative genomics. G3 (Bethesda) 15:jkaf109, 2025. Pubmed reference: 40373072. DOI: 10.1093/g3journal/jkaf109.

Tragopan temminckii (Temminck's tragopan) :

2023

Li, X., Wang, X., Yu, X., Yang, C., Lin, L., Huang, Y. :

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 24:751, 2023. Pubmed reference: 38062370. DOI: 10.1186/s12864-023-09857-6.

Tremarctos ornatus (spectacled bear) :

2021

Saremi, N.F., Oppenheimer, J., Vollmers, C., O'Connell, B., Milne, S.A., Byrne, A., Yu, L., Ryder, O.A., Green, R.E., Shapiro, B. :

An annotated draft genome for the Andean bear, Tremarctos ornatus. J Hered 112:377-384, 2021. Pubmed reference: 33882130. DOI: 10.1093/jhered/esab021.

Trematomus bernacchii (emerald rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus hansoni (striped rockcod) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus loennbergii (deepwater notothen) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trematomus scotti (blackfin notothen) :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Trichechus senegalensis (African manatee) :

2024

Huang, X., Dong, G., Fan, H., Zhou, W., Huang, G., Guan, D., Zhang, D., Wei, F. :

The genome of African manatee Trichechus senegalensis reveals secondary adaptation to the aquatic environment. iScience 27:110394, 2024. Pubmed reference: 39092175. DOI: 10.1016/j.isci.2024.110394.

Trichoglossus haematodus (coconut lorikeet) :

1991

Christidis, L., Shaw, D.D., Schodde, R. :

Chromosomal Evolution in Parrots, Lorikeets and Cockatoos (Aves, Psittaciformes). Hereditas 114:47-56, 1991.

Trichomycterus rosablanca (Andean cavefish) :

2024

Cadena, C.D., Pabón, L., DoNascimiento, C., Abueg, L., Tilley, T., O-Toole, B., Absolon, D., Sims, Y., Formenti, G., Fedrigo, O., Jarvis, E.D., Torres, M. :

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments. J Hered 115:311-316, 2024. Pubmed reference: 38513109. DOI: 10.1093/jhered/esae019.

Trichosurus vulpecula (common brushtail possum) :

2023

Bond, D.M., Ortega-Recalde, O., Laird, M.K., Hayakawa, T., Richardson, K.S., Reese, F.C.B., Kyle, B., McIsaac-Williams, B.E., Robertson, B.C., van Heezik, Y., Adams, A.L., Chang, W.S., Haase, B., Mountcastle, J., Driller, M., Collins, J., Howe, K., Go, Y., Thibaud-Nissen, F., Lister, N.C., Waters, P.D., Fedrigo, O., Jarvis, E.D., Gemmell, N.J., Alexander, A., Hore, T.A. :

The admixed brushtail possum genome reveals invasion history in New Zealand and novel imprinted genes. Nat Commun 14:6364, 2023. Pubmed reference: 37848431. DOI: 10.1038/s41467-023-41784-8.

Trimeresurus albolabris (white-lipped tree viper) :

2024

Niu, X., Lv, Y., Chen, J., Feng, Y., Cui, Y., Lu, H., Liu, H. :

The genome assembly and annotation of the white-lipped tree pit viper Trimeresurus albolabris. GigaByte 2024:gigabyte106, 2024. Pubmed reference: 38313188. DOI: 10.46471/gigabyte.106.

Triplophysa lixianensis :

2024

He, C., Zhang, X., Wen, Z., Shi, Q., Song, Z. :

A chromosome-scale reference genome assembly for Triplophysa lixianensis. Sci Data 11:1404, 2024. Pubmed reference: 39702774. DOI: 10.1038/s41597-024-04268-y.

Troides aeacus :

2024

[No authors listed] :

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860). GigaByte 2024:gigabyte122, 2024. Pubmed reference: 38707630. DOI: 10.46471/gigabyte.122.

Turdus merula (blackbird) :

2021

Kiazim, L.G., O'Connor, R.E., Larkin, D.M., Romanov, M.N., Narushin, V.G., Brazhnik, E.A., Griffin, D.K. :

Turnix suscitator (barred buttonquail) :

2023

Dey, P., Ray, S.D., Pramod, P., Singh, R.P. :

Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (Turnix suscitator). Data Brief 48:109288, 2023. Pubmed reference: 37383822. DOI: 10.1016/j.dib.2023.109288.

Tympanuchus pallidicinctus (lesser prairie-chicken) :

2023

Black, A.N., Bondo, K.J., Mularo, A., Hernandez, A., Yu, Y., Stein, C.M., Gregory, A., Fricke, K.A., Prendergast, J., Sullins, D., Haukos, D., Whitson, M., Grisham, B., Lowe, Z., DeWoody, J.A. :

A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus). Genome Biol Evol 15:evad043, 2023. Pubmed reference: 36916502. DOI: 10.1093/gbe/evad043.

Tyrannus albogularis (white-throated kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus caudifasciatus (loggerhead kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus couchii (Couch's kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus crassirostris (thick-billed kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus cubensis (giant kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus forficatus (scissor-tailed flycatcher) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus melancholicus (Tropical kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus niveigularis (snowy-throated kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus tyrannus (eastern kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus verticalis (western kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

Tyrannus vociferans (Cassin's kingbird) :

2025

Worm, A., Boves, T., Pirro, S., Sweet, A. :

The complete genome sequences of 11 species of kingbirds (Tyrannus, Tyrannidae, Passeriformes). Biodivers Genomes 2025, 2025. Pubmed reference: 40230724. DOI: 10.56179/001c.129593.

unclassified Akodon (grass mouse (unclassified)) :

1996

Aniskin, V.M., Isaev, S.I., Shchipanov, N.A. :

[Comparative cytogenetics of three species of South American field hamsters of the genus Akodon (Rodentia, Cricetidae)]. Genetika 32:83-92, 1996. Pubmed reference: 8647427.

Urocyon cinereoargenteus (gray fox) :

2024

Armstrong, E.E., Bissell, K.L., Fatima, H.S., Heikkinen, M.A., Jessup, A., Junaid, M.O., Lee, D.H., Lieb, E.C., Liem, J.T., Martin, E.M., Moreno, M., Otgonbayar, K., Romans, B.W., Royar, K., Adler, M.B., Needle, D.B., Harkess, A., Kelley, J.L., Mooney, J.A., Mychajliw, A.M. :

Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (Bethesda) 14:jkae034, 2024. Pubmed reference: 38366575. DOI: 10.1093/g3journal/jkae034.

Urosaurus nigricauda (black-tailed brush lizard) :

2023

Davalos-Dehullu, E., Baty, S.M., Fisher, R.N., Scott, P.A., Dolby, G.A., Munguia-Vega, A., Cortez, D. :

Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard. Genome Biol Evol 15:evad210, 2023. Pubmed reference: 38056449. DOI: 10.1093/gbe/evad210.

Ursidae (bears) :

2022

Willey, C., Korstanje, R. :

Sequencing and assembling bear genomes: the bare necessities. Front Zool 19:30, 2022. Pubmed reference: 36451195. DOI: 10.1186/s12983-022-00475-8.

Ursus americanus (American black bear) :

2024

Supple, M.A., Escalona, M., Adkins, J., Buchalski, M.R., Alexandre, N., Sahasrabudhe, R.M., Nguyen, O., Sacco, S., Fairbairn, C., Beraut, E., Seligmann, W., Green, R.E., Meredith, E., Shapiro, B. :

A genome assembly of the American black bear, Ursus americanus, from California. J Hered 115:498-506, 2024. Pubmed reference: 39008331. DOI: 10.1093/jhered/esae037.

2019

Srivastava, A., Kumar Sarsani, V., Fiddes, I., Sheehan, S.M., Seger, R.L., Barter, M.E., Neptune-Bear, S., Lindqvist, C., Korstanje, R. :

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation. DNA Res 26:37-44, 2019. Pubmed reference: 30395234. DOI: 10.1093/dnares/dsy036.

Ursus arctos (brown bear) :

2023

Perry, B.W., Saxton, M.W., Jansen, H.T., Quackenbush, C.R., Evans Hutzenbiler, B.D., Robbins, C.T., Kelley, J.L., Cornejo, O.E. :

A multi-tissue gene expression dataset for hibernating brown bears. BMC Genom Data 24:33, 2023. Pubmed reference: 37291509. DOI: 10.1186/s12863-023-01136-3.

2021

Scarpulla, E., Boattini, A., Cozzo, M., Giangregorio, P., Ciucci, P., Mucci, N., Randi, E., Davoli, F. :

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach. BMC Genomics 22:623, 2021. Pubmed reference: 34407764. DOI: 10.1186/s12864-021-07915-5.

Uta stansburiana :

2025

Fellows, S., Araya-Donoso, R., Dávalos-Dehullu, E., Khan, R., Weisz, D., Dudchenko, O., Aiden, E.L., Munguía-Vega, A., Dolby, G.A., Edwards, D.L. :

Chromosome-length genome assembly of Uta stansburiana and gene expression data reveal fast pace-of-life comes with environmental stability. bioRxiv , 2025. Pubmed reference: 40501859. DOI: 10.1101/2025.05.28.656178.

Varanus komodoensis (Komodo dragon) :

2019

van Hoek, M.L., Prickett, M.D., Settlage, R.E., Kang, L., Michalak, P., Vliet, K.A., Bishop, B.M. :

The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters. BMC Genomics 20:684, 2019. Pubmed reference: 31470795. DOI: 10.1186/s12864-019-6029-y.

Vicugna pacos (alpaca) :

2021

Calderon, M., More, M.J., Gutierrez, G.A., Ponce de León, F.A. :

Development of a 76k alpaca (Vicugna pacos) single nucleotide polymorphisms (SNPs) microarray. Genes (Basel) 12:291, 2021. Pubmed reference: 33669871. DOI: 10.3390/genes12020291.

2020

Mendoza, M.N., Raudsepp, T., More, M.J., Gutiérrez, G.A., Ponce de León, F.A. :

Cytogenetic mapping of 35 new markers in the alpaca (Vicugna pacos). Genes (Basel) 11:522, 2020. Pubmed reference: 32397072. DOI: 10.3390/genes11050522.

2019

Richardson, M.F., Munyard, K., Croft, L.J., Allnutt, T.R., Jackling, F., Alshanbari, F., Jevit, M., Wright, G.A., Cransberg, R., Tibary, A., Perelman, P., Appleton, B., Raudsepp, T. :

Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids. Front Genet 10:586, 2019. Pubmed reference: 31293619. DOI: 10.3389/fgene.2019.00586.

Mendoza, M.N., Raudsepp, T., Alshanbari, F., Gutiérrez, G., Ponce de León, F.A. :

Chromosomal localization of candidate genes for fiber growth and color in alpaca (Vicugna pacos). Front Genet 10:583, 2019. Pubmed reference: 31275359. DOI: 10.3389/fgene.2019.00583.

Vomeridens infuscipinnis :

2023

Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun 14:3412, 2023. Pubmed reference: 37296119. DOI: 10.1038/s41467-023-38567-6.

Vulpes lagopus (Arctic fox) :

1987

Wayne, R.K., Nash, W.G., O'Brien, S.J. :

Chromosomal evolution of the Canidae. II. Divergence from the primitive carnivore karyotype. Cytogenet Cell Genet 44:134-41, 1987. Pubmed reference: 3568762. DOI: 10.1159/000132357.

1985

Switonski, M. :

Heterochromatin heteromorphism (C-band) in the karyotype of the blue fox (Alopex lagopus). Roczniki Naukowe Zootechniki 12:29-35, 1985.

Vulpes macrotis (kit fox) :

1987

Wayne, R.K., Nash, W.G., O'Brien, S.J. :

Chromosomal evolution of the Canidae. II. Divergence from the primitive carnivore karyotype. Cytogenet Cell Genet 44:134-41, 1987. Pubmed reference: 3568762. DOI: 10.1159/000132357.

Vulpes pallida (pale fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts. Nat Ecol Evol 7:1267-1286, 2023. Pubmed reference: 37308700. DOI: 10.1038/s41559-023-02094-w.

Vulpes rueppellii (Rueppel's fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

Vulpes vulpes (red fox) :

2025

Lyu, T., Liu, Z., Xia, T., Zhou, S., Fang, J., Dong, K., Wang, L., Shi, L., Dong, Y., Sheng, Z., Wu, X., Yang, X., Zhang, H. :

The Vulpes vulpes montana genome provides insights into high-altitude adaptation mechanisms of the Vulpes species. Commun Biol 8:1070, 2025. Pubmed reference: 40681668. DOI: 10.1038/s42003-025-08450-9.

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

2019

Rando, H.M., Wadlington, W.H., Johnson, J.L., Stutchman, J.T., Trut, L.N., Farré, M., Kukekova, A.V. :

The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 10:409, 2019. Pubmed reference: 31142040. DOI: 10.3390/genes10060409.

2018

Kukekova, A.V., Johnson, J.L., Xiang, X., Feng, S., Liu, S., Rando, H.M., Kharlamova, A.V., Herbeck, Y., Serdyukova, N.A., Xiong, Z., Beklemischeva, V., Koepfli, K.P., Gulevich, R.G., Vladimirova, A.V., Hekman, J.P., Perelman, P.L., Graphodatsky, A.S., O'Brien, S.J., Wang, X., Clark, A.G., Acland, G.M., Trut, L.N., Zhang, G. :

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2:1479-1491, 2018. Pubmed reference: 30082739. DOI: 10.1038/s41559-018-0611-6.

Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nat Ecol Evol 2:1514, 2018. Pubmed reference: 30104754. DOI: 10.1038/s41559-018-0664-6.

2011

Kukekova, A.V., Trut, L.N., Chase, K., Kharlamova, A.V., Johnson, J.L., Temnykh, S.V., Oskina, I.N., Gulevich, R.G., Vladimirova, A.V., Klebanov, S., Shepeleva, D.V., Shikhevich, S.G., Acland, G.M., Lark, K.G. :

Mapping Loci for fox domestication: deconstruction/reconstruction of a behavioral phenotype. Behav Genet 41:593-606, 2011. Pubmed reference: 21153916. DOI: 10.1007/s10519-010-9418-1.

2007

Kukekova, A.V., Trut, L.N., Oskina, I.N., Johnson, J.L., Temnykh, S.V., Kharlamova, A.V., Shepeleva, D.V., Gulievich, R.G., Shikhevich, S.G., Graphodatsky, A.S., Aguirre, G.D., Acland, G.M. :

A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Res 17:387-99, 2007. Pubmed reference: 17284676. DOI: 10.1101/gr.5893307.

1998

Rubtsov, N.B. :

The Fox Gene Map. ILAR J 39:182-188, 1998. Pubmed reference: 11528077.

1995

Graphodatsky, A.S., Beklemisheva, V.R., Dolf, G. :

1987

Wayne, R.K., Nash, W.G., O'Brien, S.J. :

Chromosomal evolution of the Canidae. II. Divergence from the primitive carnivore karyotype. Cytogenet Cell Genet 44:134-41, 1987. Pubmed reference: 3568762. DOI: 10.1159/000132357.

Vulpes zerda (fennec fox) :

2023

L Rocha, J., Silva, P., Santos, N., Nakamura, M., Afonso, S., Qninba, A., Boratynski, Z., Sudmant, P.H., Brito, J.C., Nielsen, R., Godinho, R. :

Vultur gryphus (Andean condor) :

2025

De Panis, D., Le Dily, F., Lambertucci, S.A., Wiemeyer, G., Dopazo, H., Gut, M., Alioto, T.S., Mazzoni, C.J., Gut, I., Martí-Renom, M., Padró, J. :

Chromosome-scale genome assembly provides insights into condor evolution and conservation. Mol Ecol Resour 25:e70000, 2025. Pubmed reference: 40537975. DOI: 10.1111/1755-0998.70000.

Xenocypris argentea (yellowfin) :

2025

Wu, Y., Sha, H., Liang, H. :

Chromosome-scale genome assembly and annotation of Xenocypris argentea. Sci Data 12:573, 2025. Pubmed reference: 40185803. DOI: 10.1038/s41597-025-04916-x.

Xenopeltis unicolor (sunbeam snake) :

2023

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:2959-2976.e22, 2023. Pubmed reference: 37339633. DOI: 10.1016/j.cell.2023.05.030.

Peng, C., Wu, D.D., Ren, J.L., Peng, Z.L., Ma, Z., Wu, W., Lv, Y., Wang, Z., Deng, C., Jiang, K., Parkinson, C.L., Qi, Y., Zhang, Z.Y., Li, J.T. :

Large-scale snake genome analyses provide insights into vertebrate development. Cell 186:3519, 2023. Pubmed reference: 37541200. DOI: 10.1016/j.cell.2023.06.021.

Xerospermophilus spilosoma (spotted ground squirrel) :

1996

Korablev, V.P., Liapunova, E.A. :

[Variability of cytogenetic characteristics of the spotted ground squirrel Guld. 1770]. Genetika 32:79-82, 1996. Pubmed reference: 8647426.

Xiphophorus (swordtail and platyfish) :

2023

Lu, Y., Rice, E., Du, K., Kneitz, S., Naville, M., Dechaud, C., Volff, J.N., Boswell, M., Boswell, W., Hillier, L., Tomlinson, C., Milin, K., Walter, R.B., Schartl, M., Warren, W.C. :

High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 33:557-571, 2023. Pubmed reference: 37147111. DOI: 10.1101/gr.277434.122.

Xyrichtys novacula (pearly razorfish) :

2023

Cruz, F., Gómez-Garrido, J., Gut, M., Alioto, T.S., Pons, J., Alós, J., Barcelo-Serra, M. :

Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. DNA Res 30:dsad021, 2023. Pubmed reference: 37797305. DOI: 10.1093/dnares/dsad021.

Zacco platypus (freshwater minnow) :

2024

Xu, X., Chen, J., Guan, W., Niu, B., Yi, S., Lou, B. :

A chromosome-level genome assembly of East Asia endemic minnow Zacco platypus. Sci Data 11:317, 2024. Pubmed reference: 38538602. DOI: 10.1038/s41597-024-03163-w.

Nam, S.E., Rhee, J.S. :

Chromosomal-level genome assembly data from the pale chub, Zacco platypus (Jordan & Evermann, 1902). Data Brief 55:110596, 2024. Pubmed reference: 39022690. DOI: 10.1016/j.dib.2024.110596.

Zoarces viviparus (viviparous blenny) :

2024

Fuhrmann, N., Brasseur, M.V., Bakowski, C.E., Podsiadlowski, L., Prost, S., Krehenwinkel, H., Mayer, C. :

Chromosome-level genome assembly of the viviparous eelpout Zoarces viviparus. Genome Biol Evol 16:evae155, 2024. Pubmed reference: 39018026. DOI: 10.1093/gbe/evae155.

Zonotrichia capensis (rufous-collared sparrow) :

2025

Wu, Z., Miedzinska, K., Krause, J.S., Gonzalez-Gomez, P.L., Pérez, J.H., Wingfield, J.C., Meddle, S.L., Smith, J. :

Genome assemblies of Nuttall's White-crowned sparrow (Zonotrichia leucophrys nuttalli) and Rufous-collared sparrow (Zonotrichia capensis). Sci Data 12:567, 2025. Pubmed reference: 40180969. DOI: 10.1038/s41597-025-04889-x.

Zonotrichia leucophrys :

2025

Wu, Z., Miedzinska, K., Krause, J.S., Gonzalez-Gomez, P.L., Pérez, J.H., Wingfield, J.C., Meddle, S.L., Smith, J. :

2024

Wu, Z., Miedzinska, K., Krause, J.S., Pérez, J.H., Wingfield, J.C., Meddle, S.L., Smith, J. :

A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii). Sci Data 11:86, 2024. Pubmed reference: 38238322. DOI: 10.1038/s41597-024-02929-6.

The University of Sydney - OMIA - Online Mendelian Inheritance in Animals

Genetic Resources

Acanthopagrus schlegelii (black porgy) :

Acestrorhynchus altus :

Acinonyx jubatus (cheetah) :

Acomys cahirinus (Egyptian spiny mouse) :

Acridotheres tristis (common myna) :

Acrossocheilus fasciatus :

Actinemys marmorata (Pacific pond turtle) :

Actinopterygii (ray-finned fishes) :

Addax nasomaculatus :

Agapornis :

Agapornis roseicollis (peach-faced lovebird) :

Agelaius tricolor (tricolored blackbird) :

Ahaetulla prasina (Asian vine snakes) :

Ailuropoda melanoleuca (giant panda) :

Akarotaxis nudiceps :

Akodon simulator (White-throated Akodont) :

Akodon toba (Chaco grass mouse) :

Albula glossodonta (roundjaw bonefish) :

Alces alces (Eurasian elk) :

Alectoris barbara (Barbary partridge) :

Alectoris chukar (chukar partridge) :

Alectoris magna (Przewalski's partridge) :

Alectoris rufa (red-legged partridge) :

Alisterus scapularis :

Alligator mississippiensis (American alligator) :

Alosa sapidissima (American shad) :

Amazona aestiva (blue-fronted amazon) :

Amazona vittata (Puerto Rican parrot) :

Amblyraja radiata (thorny skate) :

Amia calva (bowfin) :

Amphibia (amphibians) :

Amphilophus citrinellus (Midas cichlid) :

Amphiprion bicinctus (twoband anemonefish) :

Amphiprion percula (orange clownfish) :

Anarhynchus dealbatus (White-faced plover) :

Anas acuta (northern pintail) :

Anas crecca (Common teal) :

Anas platyrhynchos (Mallard) :

Anas platyrhynchos x Cairina moschata (domestic duck x muscovy duck) :

Anas zonorhyncha (eastern spot-billed duck) :

Anatidae (waterfowl) :

Andrias davidianus (Chinese giant salamander) :

Anguilla bicolor (Indonesian shortfin eel) :

Anisarchus medius (stout eelblenny) :

Anolis apletophallus (slender anole) :

Anomalopteryx didiformis (little bush moa) :

Anoplopoma fimbria (sablefish) :

Anser anser (domestic goose) :

Anser cygnoides (swan goose) :

Antennarius striatus (striated frogfish) :

Antidorcas marsupialis (springbok) :

Antilope cervicapra (blackbuck) :

Apareiodon sp. 'Rio Verde' :

Aphelocoma californica (Western scrub-jay) :

Aphelocoma coerulescens (scrub jay) :

Apis mellifera (honey bee) :

Apricaphanius iberus (Spanish toothcarp) :

Aquarana catesbeiana (bullfrog) :

Ara macao (scarlet macaw) :

Aratinga solstitialis (sun parakeet) :

Archilochus colubris :

Archocentrus centrarchus (flier cichlid) :

Arctocephalus gazella (antarctic fur seal) :

Argyrosomus japonicus (mulloway) :

Ariidae (sea catfishes) :

Arizona elegans occidentalis :

Asaccus caudivolvulus :

Aselliscus stoliczkanus (Stoliczka's Asian trident bat) :

Asio madagascariensis :

Astatotilapia calliptera (eastern happy) :

Astyanax mexicanus (Mexican tetra) :

Atelerix albiventris (middle-African hedgehog) :

Ateles fusciceps (brown-headed spider monkey) :

Ateles paniscus (black spider monkey) :

Atelopus laetissimus (Santa Marta harlequin toad) :

Atractosteus spatula (alligator gar) :

Aythya baeri (Baer's pochard) :

Aythya ferina (common pochard) :