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Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations

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dc.contributor.author Koepfli, Klaus-Peter en
dc.contributor.author Tamazian, Gaik en
dc.contributor.author Wildt, David E. en
dc.contributor.author Dobrynin, Pavel en
dc.contributor.author Kim, Changhoon en
dc.contributor.author Frandsen, Paul B. en
dc.contributor.author Godinho, Raquel en
dc.contributor.author Yurchenko, Andrey A. en
dc.contributor.author Komissarov, Aleksey en
dc.contributor.author Krasheninnikova, Ksenia en
dc.contributor.author Kliver, Sergei en
dc.contributor.author Kolchanova, Sofia en
dc.contributor.author Gonçalves, Margarida en
dc.contributor.author Carneiro, Miguel en
dc.contributor.author Vaz Pinto, Pedro en
dc.contributor.author Ferrand, Nuno en
dc.contributor.author Maldonado, Jesús E. en
dc.contributor.author Ferrie, Gina M. en
dc.contributor.author Chemnick, Leona en
dc.contributor.author Ryder, Oliver A. en
dc.contributor.author Johnson, Warren E. en
dc.contributor.author Comizzoli, Pierre en
dc.contributor.author O'Brien, Stephen J. en
dc.contributor.author Pukazhenthi, Budhan S. en
dc.date.accessioned 2019-05-02T02:04:18Z
dc.date.available 2019-05-02T02:04:18Z
dc.date.issued 2019
dc.identifier.citation Koepfli, Klaus-Peter, Tamazian, Gaik, Wildt, David E., Dobrynin, Pavel, Kim, Changhoon, Frandsen, Paul B., Godinho, Raquel, Yurchenko, Andrey A., Komissarov, Aleksey, Krasheninnikova, Ksenia, Kliver, Sergei, Kolchanova, Sofia, Gonçalves, Margarida, Carneiro, Miguel, Vaz Pinto, Pedro, Ferrand, Nuno, Maldonado, Jesús E., Ferrie, Gina M., Chemnick, Leona, Ryder, Oliver A., Johnson, Warren E., Comizzoli, Pierre, O'Brien, Stephen J., and Pukazhenthi, Budhan S. 2019. "<a href="https://repository.si.edu/handle/10088/96493">Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations</a>." <em>G3 (Bethesda, Md.)</em>. 9 (6):1785&ndash;1793. <a href="https://doi.org/10.1534/g3.119.400084">https://doi.org/10.1534/g3.119.400084</a> en
dc.identifier.issn 2160-1836
dc.identifier.uri https://hdl.handle.net/10088/96493
dc.description.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 2.926 Gb draft genome consists of 136,532 contigs with an N50 of 45.5 Kbp and 16,931 scaffolds with an N50 of 4.59 Mbp. De novo annotation identified 21,276 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. en
dc.relation.ispartof G3 (Bethesda, Md.) en
dc.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 en
dc.type Journal Article en
dc.identifier.srbnumber 151008
dc.identifier.doi 10.1534/g3.119.400084
rft.jtitle G3 (Bethesda, Md.)
rft.volume 9
rft.issue 6
rft.spage 1785
rft.epage 1793
dc.description.SIUnit NZP en
dc.citation.spage 1785
dc.citation.epage 1793


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