Genomic legacy of the African cheetah, Acinonyx jubatus
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- Genomic legacy of the African cheetah, Acinonyx jubatus
- Dobrynin, Pavel; Liu, Shiping; Tamazian, Gaik; Xiong, Zijun; Yurchenko, Andrey A.; Krasheninnikova, Ksenia; Kliver, Sergey; Schmidt-K&uuml;ntzel, Anne; Koepfli, Klaus-Peter; Johnson, Warren; Kuderna, Lukas F.K.; Garc&iacute;a-P&eacute;rez, Raquel; Manuel, Marc de; 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; Marques-Bonet, Tomas; Marker, Laurie; Bhak, Jong Hwa; Wang, Jun; Zhang, Guojie; O'Brien, Stephen J.
- Issue Date
- BIOMED CENTRAL LTD
- GENOME BIOLOGY, v.16, no.1, pp.277
- 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.
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