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Genomic legacy of the African cheetah, Acinonyx jubatus

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 ge...

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Autores principales: Dobrynin, Pavel, Liu, Shiping, Tamazian, Gaik, Xiong, Zijun, Yurchenko, Andrey A., Krasheninnikova, Ksenia, Kliver, Sergey, Schmidt-Küntzel, Anne, Koepfli, Klaus-Peter, Johnson, Warren, 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, Perelman, Polina, Roelke, Melody, Wildt, David, Diekhans, Mark, Marques-Bonet, Tomas, Marker, Laurie, Bhak, Jong, Wang, Jun, Zhang, Guojie, O’Brien, Stephen J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/
https://www.ncbi.nlm.nih.gov/pubmed/26653294
http://dx.doi.org/10.1186/s13059-015-0837-4
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author Dobrynin, Pavel
Liu, Shiping
Tamazian, Gaik
Xiong, Zijun
Yurchenko, Andrey A.
Krasheninnikova, Ksenia
Kliver, Sergey
Schmidt-Küntzel, Anne
Koepfli, Klaus-Peter
Johnson, Warren
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
Perelman, Polina
Roelke, Melody
Wildt, David
Diekhans, Mark
Marques-Bonet, Tomas
Marker, Laurie
Bhak, Jong
Wang, Jun
Zhang, Guojie
O’Brien, Stephen J.
author_facet Dobrynin, Pavel
Liu, Shiping
Tamazian, Gaik
Xiong, Zijun
Yurchenko, Andrey A.
Krasheninnikova, Ksenia
Kliver, Sergey
Schmidt-Küntzel, Anne
Koepfli, Klaus-Peter
Johnson, Warren
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
Perelman, Polina
Roelke, Melody
Wildt, David
Diekhans, Mark
Marques-Bonet, Tomas
Marker, Laurie
Bhak, Jong
Wang, Jun
Zhang, Guojie
O’Brien, Stephen J.
author_sort Dobrynin, Pavel
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0837-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-46761272015-12-12 Genomic legacy of the African cheetah, Acinonyx jubatus Dobrynin, Pavel Liu, Shiping Tamazian, Gaik Xiong, Zijun Yurchenko, Andrey A. Krasheninnikova, Ksenia Kliver, Sergey Schmidt-Küntzel, Anne Koepfli, Klaus-Peter Johnson, Warren 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 Perelman, Polina Roelke, Melody Wildt, David Diekhans, Mark Marques-Bonet, Tomas Marker, Laurie Bhak, Jong Wang, Jun Zhang, Guojie O’Brien, Stephen J. Genome Biol Research 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0837-4) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-10 2015 /pmc/articles/PMC4676127/ /pubmed/26653294 http://dx.doi.org/10.1186/s13059-015-0837-4 Text en © Dobrynin et al. 2015 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 made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Dobrynin, Pavel
Liu, Shiping
Tamazian, Gaik
Xiong, Zijun
Yurchenko, Andrey A.
Krasheninnikova, Ksenia
Kliver, Sergey
Schmidt-Küntzel, Anne
Koepfli, Klaus-Peter
Johnson, Warren
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
Perelman, Polina
Roelke, Melody
Wildt, David
Diekhans, Mark
Marques-Bonet, Tomas
Marker, Laurie
Bhak, Jong
Wang, Jun
Zhang, Guojie
O’Brien, Stephen J.
Genomic legacy of the African cheetah, Acinonyx jubatus
title Genomic legacy of the African cheetah, Acinonyx jubatus
title_full Genomic legacy of the African cheetah, Acinonyx jubatus
title_fullStr Genomic legacy of the African cheetah, Acinonyx jubatus
title_full_unstemmed Genomic legacy of the African cheetah, Acinonyx jubatus
title_short Genomic legacy of the African cheetah, Acinonyx jubatus
title_sort genomic legacy of the african cheetah, acinonyx jubatus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/
https://www.ncbi.nlm.nih.gov/pubmed/26653294
http://dx.doi.org/10.1186/s13059-015-0837-4
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