Genomic legacy of the African cheetah, Acinonyx jubatus

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• dc.contributor.author Dobrynin, Pavelca
• dc.contributor.author Kuderna, Lukas, 1989-ca
• dc.contributor.author García Pérez, Raquel, 1989-ca
• dc.contributor.author de Manuel, Marcca
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
• dc.contributor.author O’Brien, Stephen J.ca
• dc.date.accessioned 2016-01-26T15:08:24Z
• dc.date.available 2016-01-26T15:08:24Z
• 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.ca
• 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).
• dc.format.mimetype application/pdfca
• dc.identifier.citation Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K et al. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome biology. 2015;16:277. DOI 10.1186/s13059-015-0837-4ca
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0837-4
• dc.identifier.issn 1664-042X
• dc.identifier.uri http://hdl.handle.net/10230/25662
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome biology. 2015;16:277
• dc.relation.projectID info:eu‐repo/grantAgreement/ES/1PE/BFU2014-55090-P
• 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
• dc.subject.keyword Genetic diversity
• dc.subject.keyword Conservation biology
• dc.subject.keyword Population biology
• dc.subject.other Biologia de la conservacióca
• dc.subject.other Genèticaca
• dc.title Genomic legacy of the African cheetah, Acinonyx jubatusca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca