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Genomic legacy of the African cheetah, Acinonyx jubatus

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dc.contributor.author Dobrynin, Pavel
dc.contributor.author Liu, Shiping
dc.contributor.author Tamazian, Gaik
dc.contributor.author Xiong, Zijun
dc.contributor.author Yurchenko, Andrey A.
dc.contributor.author Krasheninnikova, Ksenia
dc.contributor.author Kliver, Sergey
dc.contributor.author Schmidt-Küntzel, Anne
dc.contributor.author Koepfli, Klaus-Peter
dc.contributor.author Johnson, Warren
dc.contributor.author Kuderna, Lukas, 1989-
dc.contributor.author García Pérez, Raquel, 1989-
dc.contributor.author de Manuel, Marc
dc.contributor.author Godinez, Ricardo
dc.contributor.author Komissarov, Aleksey
dc.contributor.author Makunin, Alexey
dc.contributor.author Brukhin, Vladimir
dc.contributor.author Qiu, Weilin
dc.contributor.author Zhou, Long
dc.contributor.author Li, Fang
dc.contributor.author Yi, Jian
dc.contributor.author Driscoll, Carlos
dc.contributor.author Antunes, Agostinho
dc.contributor.author Oleksyk, Taras K.
dc.contributor.author Eizirik, Eduardo
dc.contributor.author Perelman, Polina
dc.contributor.author Roelke, Melody
dc.contributor.author Wildt, David
dc.contributor.author Diekhans, Mark
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Marker, Laurie
dc.contributor.author Bhak, Jong
dc.contributor.author Wang, Jun
dc.contributor.author Zhang, Guojie
dc.contributor.author O'Brien, Stephen J.
dc.date.accessioned 2018-06-07T07:52:02Z
dc.date.available 2018-06-07T07:52:02Z
dc.date.issued 2015
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.issn 1474-760X
dc.identifier.uri http://hdl.handle.net/10230/34845
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.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Genome Biology. 2015;16:277
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.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 jubatus
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0837-4
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-6215-ERC
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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