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Genomic legacy of the African cheetah, Acinonyx jubatus

Catalog Data

Author:
Wildt, David E.  Search this
Perelman, Polina  Search this
Zhang, Guojie  Search this
Koepfli, Klaus-Peter  Search this
Xiong, Zijun  Search this
Zhou, Long  Search this
O'Brien, Stephen J.  Search this
Marker, Laurie  Search this
Schmidt-Küntzel, Anne  Search this
Eizirik, Eduardo  Search this
Makunin, Alexey  Search this
Antunes, Agostinho  Search this
Dobrynin, Pavel  Search this
Yi, Jian  Search this
Driscoll, Carlos  Search this
Tamazian, Gaik  Search this
García-Pérez, Raquel  Search this
Godinez, Ricardo  Search this
Kliver, Sergey  Search this
Diekhans, Mark  Search this
Bhak, Jong  Search this
Brukhin, Vladimir  Search this
Oleksyk, Taras K.  Search this
Yurchenko, Andrey A.  Search this
Krasheninnikova, Ksenia  Search this
Kuderna, Lukas F. K.  Search this
Marques-Bonet, Tomas  Search this
Roelke, Melody  Search this
Qiu, Weilin  Search this
Komissarov, Aleksey  Search this
Li, Fang  Search this
Liu, Shiping  Search this
Manuel, Marc de  Search this
Johnson, Warren E.  Search this
Wang, Jun  Search this
Object Type:
Smithsonian staff publication
Electronic document
Year:
2015
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 (p80 %) 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.
Doi:
10.1186/s13059-015-0837-4
Citation:
Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Küntzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren E., Kuderna, Lukas F. K., García-Pérez, 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, et al. 2015. Genomic legacy of the African cheetah, Acinonyx jubatus. <i>Genome biology<i>, 16: 277 doi:10.1186/s13059-015-0837-4
Topic:
Zoology  Search this
Animals  Search this
Veterinary medicine  Search this
Animal health  Search this
Data source:
Smithsonian Libraries
EDAN-URL:
edanmdm:SILSRO_138616