Biology Faculty Articles

Title

Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A resource for monitoring diversity in ex situ and in situ populations

Authors

Klaus Peter Koepfli, Conservation and Research Center (National Zoo)
Gaik Tamazian, Saint Petersburg State University
David Wildt, Conservation and Research Center (National Zoo)
Pavel Dobrynin, Conservation and Research Center (National Zoo)
Changhoon Kim, Macrogen, Inc.
Paul B. Frandsen, Brigham Young University
Raquel Godinho, Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos
Andrey A. Yurchenko, Saint Petersburg State University
Aleksey Komissarov, Saint Petersburg State University
Ksenia Krasheninnikova, Saint Petersburg State University
Sergei Kliver, Saint Petersburg State University
Sofia Kolchanova, Saint Petersburg State University
Margarida Gonçalves, Universidade do Porto
Miguel Carneiro, Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos
Pedro Vaz Pinto, Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos
Nuno Ferrand, Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos
Jesús E. Maldonado, National Zoological Park
Gina M. Ferrie, Disney's Animal Kingdom
Leona Chemnick, San Diego Zoo Institute for Conservation Research
Oliver A. Ryder, San Diego Zoo Institute for Conservation Research
Warren E. Johnson, Conservation and Research Center (National Zoo)
Pierre Comizzoli, Conservation and Research Center (National Zoo)
Stephen J. O'Brien, Saint Petersburg State UniversityFollow
Budhan S. Pukazhenthi, Conservation and Research Center (National Zoo)

Document Type

Article

Publication Date

1-1-2019

Publication Title

G3: Genes, Genomes, Genetics

Keywords

Assembly, Bovidae, Conservation, Genetics, Genome, Hippotragus, Niger, Sable antelope

ISSN

21601836

Volume

9

Issue/No.

6

First Page

1785

Last Page

1793

Abstract

Genome-wide assessment of genetic diversity has the potential to increase the ability to understand admixture, inbreeding, kinship and erosion of genetic diversity affecting both captive (ex situ) and wild (in situ) populations of threatened species. The sable antelope (Hippotragus niger), native to the savannah woodlands of sub-Saharan Africa, is a species that is being managed ex situ in both public (zoo) and private (ranch) collections in the United States. Our objective was to develop whole genome sequence resources that will serve as a foundation for characterizing the genetic status of ex situ populations of sable antelope relative to populations in the wild. Here we report the draft genome assembly of a male sable antelope, a member of the subfamily Hippotraginae (Bovidae, Cetartiodactyla, Mammalia). The 2.596 Gb draft genome consists of 136,528 contigs with an N50 of 45.5 Kbp and 16,927 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 18,828 protein-coding genes and repetitive sequences encompassing 46.97% of the genome. The discovery of single nucleotide variants (SNVs) was assisted by the re-sequencing of seven additional captive and wild individuals, representing two different subspecies, leading to the identification of 1,987,710 bi-allelic SNVs. Assembly of the mitochondrial genomes revealed that each individual was defined by a unique haplotype and these data were used to infer the mitochondrial gene tree relative to other hippotragine species. The sable antelope genome constitutes a valuable resource for assessing genome-wide diversity and evolutionary potential, thereby facilitating long-term conservation of this charismatic species.

DOI

10.1534/g3.119.400084

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