Genomic legacy of the African cheetah, Acinonyx jubatus

  • December 14, 2014
  • by P. Dobrynin, S. Liu, G. Tamazian, Z. Xiong, A.A. Yurchenko, K. Krasheninnikova, S. Kliver, A. Schmidt-Küntzel, K. Koepfli, W.E. Johnson, L.F.K. Kuderna, R. Garcia-Perez, M. Manuel, R. Godinez, A. Komissarov, A. Makunin, V. Brukhin, W. Qiu, L. Zhou, F. Li, J. Yi, C. Dricoll, A. Antunes, T.K. Oleksyk, E. Eizirik, P. Perelman, D.E. Wildt, M. Diekhans, T. Marques-Bonet, L.L. Marker, J. Bhak, J. Wang, G. Zhang, S.J. O'Brien



Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.


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.


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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