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Bhak, Jong
The Genomics Institute of UNIST (TGI)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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Genomic legacy of the African cheetah, Acinonyx jubatus

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Title
Genomic legacy of the African cheetah, Acinonyx jubatus
Author
Dobrynin, PavelLiu, ShipingTamazian, GaikXiong, ZijunYurchenko, Andrey A.Krasheninnikova, KseniaKliver, SergeySchmidt-Küntzel, AnneKoepfli, Klaus-PeterJohnson, WarrenKuderna, Lukas F.K.García-Pérez, RaquelManuel, Marc deGodinez, RicardoKomissarov, AlekseyMakunin, AlexeyBrukhin, VladimirQiu, WeilinZhou, LongLi, FangYi, JianDriscoll, CarlosAntunes, AgostinhoOleksyk, Taras K.Eizirik, EduardoPerelman, PolinaRoelke, MelodyWildt, DavidDiekhans, MarkMarques-Bonet, TomasMarker, LaurieBhak, Jong HwaWang, JunZhang, GuojieO'Brien, Stephen J.
Keywords
Conservation biology; Genetic diversity; Population biology
Issue Date
201512
Publisher
BIOMED CENTRAL LTD
Citation
GENOME BIOLOGY, v.16, no.1, pp.277 -
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. © 2015 Dobrynin et al
URI
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DOI
http://dx.doi.org/10.1186/s13059-015-0837-4
ISSN
1474-760X
Appears in Collections:
SLS_Journal Papers
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