Research output: Contribution to journal › Article › peer-review
Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger) : A resource for monitoring diversity in ex situ and in situ populations. / Koepfli, Klaus Peter; Tamazian, Gaik; Wildt, David; Dobrynin, Pavel; Kim, Changhoon; Frandsen, Paul B.; Godinho, Raquel; Yurchenko, Andrey A.; Komissarov, Aleksey; Krasheninnikova, Ksenia; Kliver, Sergei; Kolchanova, Sofia; Gonçalves, Margarida; Carneiro, Miguel; Pinto, Pedro Vaz; Ferrand, Nuno; Maldonado, Jesús E.; Ferrie, Gina M.; Chemnick, Leona; Ryder, Oliver A.; Johnson, Warren E.; Comizzoli, Pierre; O'Brien, Stephen J.; Pukazhenthi, Budhan S.
In: G3 (Bethesda, Md.), Vol. 9, No. 6, 05.06.2019, p. 1785-1793.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger)
T2 - A resource for monitoring diversity in ex situ and in situ populations
AU - Koepfli, Klaus Peter
AU - Tamazian, Gaik
AU - Wildt, David
AU - Dobrynin, Pavel
AU - Kim, Changhoon
AU - Frandsen, Paul B.
AU - Godinho, Raquel
AU - Yurchenko, Andrey A.
AU - Komissarov, Aleksey
AU - Krasheninnikova, Ksenia
AU - Kliver, Sergei
AU - Kolchanova, Sofia
AU - Gonçalves, Margarida
AU - Carneiro, Miguel
AU - Pinto, Pedro Vaz
AU - Ferrand, Nuno
AU - Maldonado, Jesús E.
AU - Ferrie, Gina M.
AU - Chemnick, Leona
AU - Ryder, Oliver A.
AU - Johnson, Warren E.
AU - Comizzoli, Pierre
AU - O'Brien, Stephen J.
AU - Pukazhenthi, Budhan S.
PY - 2019/6/5
Y1 - 2019/6/5
N2 - 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.
AB - 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.
KW - Биоинформатика
KW - Animals
KW - Antelopes/classification
KW - Biodiversity
KW - Biological Evolution
KW - Computational Biology/methods
KW - Female
KW - Genetic Variation
KW - Genetics, Population
KW - Genome
KW - Genome, Mitochondrial
KW - Genomics/methods
KW - Male
KW - Molecular Sequence Annotation
KW - Phenotype
KW - Phylogeny
KW - United States
KW - Whole Genome Sequencing
UR - http://www.scopus.com/inward/record.url?scp=85067127074&partnerID=8YFLogxK
U2 - doi: 10.1534/g3.119.400084.
DO - doi: 10.1534/g3.119.400084.
M3 - Article
C2 - 31000506
AN - SCOPUS:85067127074
VL - 9
SP - 1785
EP - 1793
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
SN - 2160-1836
IS - 6
ER -
ID: 49509949