Genomic legacy of the African cheetah, Acinonyx jubatus

Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-Küntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Kuderna, Lukas, 1989-; García Pérez, Raquel, 1989-; de Manuel, Marc; Godinez, Ricardo; Komissarov, Aleksey; Makunin, Alexey; Brukhin, Vladimir; Qiu, Weilin; Zhou, Long; Li, Fang; Yi, Jian; Driscoll, Carlos; Antunes, Agostinho; Oleksyk, Taras K.; Eizirik, Eduardo; Perelman, Polina; Roelke, Melody; Wildt, David; Diekhans, Mark; Marquès i Bonet, Tomàs, 1975-; Marker, Laurie; Bhak, Jong; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J.

Genomic legacy of the African cheetah, Acinonyx jubatus

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dc.contributor.author Dobrynin, Pavelca
dc.contributor.author Liu, Shipingca
dc.contributor.author Tamazian, Gaikca
dc.contributor.author Xiong, Zijunca
dc.contributor.author Yurchenko, Andrey A.ca
dc.contributor.author Krasheninnikova, Kseniaca
dc.contributor.author Kliver, Sergeyca
dc.contributor.author Schmidt-Küntzel, Anneca
dc.contributor.author Koepfli, Klaus-Peterca
dc.contributor.author Johnson, Warrenca
dc.contributor.author Kuderna, Lukas, 1989-ca
dc.contributor.author García Pérez, Raquel, 1989-ca
dc.contributor.author de Manuel, Marcca
dc.contributor.author Godinez, Ricardoca
dc.contributor.author Komissarov, Alekseyca
dc.contributor.author Makunin, Alexeyca
dc.contributor.author Brukhin, Vladimirca
dc.contributor.author Qiu, Weilinca
dc.contributor.author Zhou, Longca
dc.contributor.author Li, Fangca
dc.contributor.author Yi, Jianca
dc.contributor.author Driscoll, Carlosca
dc.contributor.author Antunes, Agostinhoca
dc.contributor.author Oleksyk, Taras K.ca
dc.contributor.author Eizirik, Eduardoca
dc.contributor.author Perelman, Polinaca
dc.contributor.author Roelke, Melodyca
dc.contributor.author Wildt, Davidca
dc.contributor.author Diekhans, Markca
dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
dc.contributor.author Marker, Laurieca
dc.contributor.author Bhak, Jongca
dc.contributor.author Wang, Junca
dc.contributor.author Zhang, Guojieca
dc.contributor.author O'Brien, Stephen J.ca
dc.date.accessioned 2018-06-07T07:52:02Z
dc.date.available 2018-06-07T07:52:02Z
dc.date.issued 2015
dc.description.abstract BACKGROUND: Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS: Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084-12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah's extremely high (>80 %) pleiomorphic sperm. CONCLUSIONS:The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species' natural history, physiological adaptations and unique reproductive disposition.
dc.description.sponsorship This work was supported in part by a Russian Ministry of Science Mega-grant (no 11.G34.31.0068), a St. Petersburg State University grant (no 1.50.1623.2013), an ICREA grant (no. BFU2014-55090-P), an EMBO YIP 2013 grant (no. BFU2015-7116-ERC) and an MICINN grant (no. BFU2015-6215-ERC). Sample collection and validation of reproductive genes were performed under the permit number 1833/2013, granted by the Namibian Ministry of Environment and Tourism
dc.format.mimetype application/pdf
dc.identifier.citation Klus P, Ponti R, Livi C, Tartaglia G. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biology. 2015;16:277. DOI: 10.1186/s13059-015-0837-4
dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0837-4
dc.identifier.issn 1474-760X
dc.identifier.uri http://hdl.handle.net/10230/34845
dc.language.iso eng
dc.publisher BioMed Centralca
dc.relation.ispartof Genome Biology. 2015;16:277
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-6215-ERC
dc.rights © 2015 Dobrynin et al. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Acinonyx
dc.subject.other Genomes
dc.title Genomic legacy of the African cheetah, Acinonyx jubatusca
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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