Biology Faculty Articles

Authors

Pavel Dobrynin, St. Petersburg State University - Russia
Shiping Liu, BGI-Shenzhen - China; Sun Yat-sen University - China
Gaik Tamazian, St. Petersburg State University - Russia
Zijun Xiong, BGI-Shenzhen - China
Andrey A. Yurchenko, St. Petersburg State University - Russia
Ksenia Krasheninnikova, St. Petersburg State University - Russia
Sergey Kliver, St. Petersburg State University - Russia
A. Schmidt-Kunzel, Cheetah Conservation Fund - Namibia
Klaus-Peter Koepfli, Smithsonian Conservation Biology Institute; St. Petersburg State University - Russia
Warren E. Johnson, Smithsonian Conservation Biology Institute
Lukas F. K. Kuderna, Institut de Biologia Evolutiva - Barcelona, Spain
Raquel Garcia-Perez, Institut de Biologia Evolutiva - Barcelona, Spain
Marc de Manuel, Institut de Biologia Evolutiva - Barcelona, Spain
Ricardo Godinez, Harvard University
Aleksey Komissarov, St. Petersburg State University - Russia
Alexey Makunin, St. Petersburg State University - Russia; Russian Academy of Sciences
Vladimir Brukhin, St. Petersburg State University - Russia
Weilin Qiu, BGI-Shenzhen - China
Long Zhou, BGI-Shenzhen - China
Fang Li, BGI-Shenzhen - China
Jian Yi, BGI-Shenzhen - China
Carlos A. Driscoll, National Institute on Alcohol Abuse and Alcoholism
Agostinho Antunes, Universidade do Porto - Portugal
T. K. Oleksyk, University of Puerto Rico at Mayaguez
Eduardo Eizirik, PUCRS - Brazil
Polina Perelman, Russian Academy of Sciences; Novosibirsk State University - Russia
Melody E. Roelke, Leidos Biomedical Research Inc.
David E. Wildt, National Zoological Park - Washington, D.C.
Mark Diekhans, University of California - Santa Cruz
Tomas Marques-Bonet, Institut de Biologia Evolutiva - Barcelona, Spain; Centro Nacional de Analisis Genomics - Barcelona, Spain; Sun Yat-sen University - China
Laurie Marker, Cheetah Conservation Fund - Namibia
Jong Bhak, Ulsan National Institute of Science and Technology - Republic of Korea
Jun Wang, BGI-Shenzhen - China; University of Copenhagen - Denmark; King Abdulaziz University - Saudi Arabia; Macau University of Science and Technology - China
Guojie Zhang, BGI-Shenzhen - China; University of Copenhagen - Denmark
Stephen J. O'Brien, St. Petersburg State University - Russia; Nova Southeastern UniversityFollow

Document Type

Article

Publication Date

12-10-2015

Publication Title

Genome Biology

Keywords

Genetic diversity, Conservation biology, Population biology

ISSN

1474-760X

Volume

16

Issue/No.

277

First Page

1

Last Page

19

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.

Comments

© 2015 Dobrynin et al. 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.

Additional Comments

Russian Ministry of Science grant #: 11.G34.31.0068; St. Petersburg State University grant #: 1.50.1623.2013; ICREA grant #: BFU2014-55090-P; EMBO YIP 2013 grant #: BFU2015- 7116-ERC; MICINN grant #: BFU2015-6215-ERC; GenBank accession #: LLWD01000000

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

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