Dobrynin, PavelLiu, ShipingTamazian, GaikXiong, ZijunYurchenko, Andrey A.Krasheninnikova, KseniaKliver, SergeySchmidt-Küntzel, AnneKoepfli, Klaus-PeterJohnson, WarrenKuderna, Lukas, 1989-García Pérez, Raquel, 1989-de Manuel, MarcGodinez, RicardoKomissarov, AlekseyMakunin, AlexeyBrukhin, VladimirQiu, WeilinZhou, LongLi, FangYi, JianDriscoll, CarlosAntunes, AgostinhoOleksyk, Taras K.Eizirik, EduardoPerelman, PolinaRoelke, MelodyWildt, DavidDiekhans, MarkMarquès i Bonet, Tomàs, 1975-Marker, LaurieBhak, JongWang, JunZhang, GuojieO'Brien, Stephen J.2018-06-072018-06-072015Klus P, Ponti R, Livi C, Tartaglia G. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biology. 2015;16:277. DOI: 10.1186/s13059-015-0837-41474-760Xhttp://hdl.handle.net/10230/34845BACKGROUND: 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.application/pdfeng© 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 madeAcinonyxGenomesinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13059-015-0837-4info:eu-repo/semantics/openAccess