Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2019-06-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.119.400084 |
| _version_ | 1818436754655412224 |
|---|---|
| author | Klaus-Peter Koepfli Gaik Tamazian David Wildt Pavel Dobrynin Changhoon Kim Paul B. Frandsen Raquel Godinho Andrey A. Yurchenko Aleksey Komissarov Ksenia Krasheninnikova Sergei Kliver Sofia Kolchanova Margarida Gonçalves Miguel Carneiro Pedro Vaz Pinto Nuno Ferrand Jesús E. Maldonado Gina M. Ferrie Leona Chemnick Oliver A. Ryder Warren E. Johnson Pierre Comizzoli Stephen J. O’Brien Budhan S. Pukazhenthi |
| author_facet | Klaus-Peter Koepfli Gaik Tamazian David Wildt Pavel Dobrynin Changhoon Kim Paul B. Frandsen Raquel Godinho Andrey A. Yurchenko Aleksey Komissarov Ksenia Krasheninnikova Sergei Kliver Sofia Kolchanova Margarida Gonçalves Miguel Carneiro Pedro Vaz Pinto Nuno Ferrand Jesús E. Maldonado Gina M. Ferrie Leona Chemnick Oliver A. Ryder Warren E. Johnson Pierre Comizzoli Stephen J. O’Brien Budhan S. Pukazhenthi |
| author_sort | Klaus-Peter Koepfli |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T17:13:48Z |
| format | Article |
| id | doaj.art-331b91f49f3f46c289ee32b9ce98c48c |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-14T17:13:48Z |
| publishDate | 2019-06-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-331b91f49f3f46c289ee32b9ce98c48c2022-12-21T22:53:28ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362019-06-01961785179310.1534/g3.119.4000841Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ PopulationsKlaus-Peter KoepfliGaik TamazianDavid WildtPavel DobryninChanghoon KimPaul B. FrandsenRaquel GodinhoAndrey A. YurchenkoAleksey KomissarovKsenia KrasheninnikovaSergei KliverSofia KolchanovaMargarida GonçalvesMiguel CarneiroPedro Vaz PintoNuno FerrandJesús E. MaldonadoGina M. FerrieLeona ChemnickOliver A. RyderWarren E. JohnsonPierre ComizzoliStephen J. O’BrienBudhan S. PukazhenthiGenome-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.http://g3journal.org/lookup/doi/10.1534/g3.119.400084Hippotragus nigersable antelopegenome assemblyconservation geneticsBovidae |
| spellingShingle | Klaus-Peter Koepfli Gaik Tamazian David Wildt Pavel Dobrynin Changhoon Kim Paul B. Frandsen Raquel Godinho Andrey A. Yurchenko Aleksey Komissarov Ksenia Krasheninnikova Sergei Kliver Sofia Kolchanova Margarida Gonçalves Miguel Carneiro Pedro Vaz Pinto Nuno Ferrand Jesús E. Maldonado Gina M. Ferrie Leona Chemnick Oliver A. Ryder Warren E. Johnson Pierre Comizzoli Stephen J. O’Brien Budhan S. Pukazhenthi Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations G3: Genes, Genomes, Genetics Hippotragus niger sable antelope genome assembly conservation genetics Bovidae |
| 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 |
| title_full | Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations |
| title_fullStr | Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations |
| title_full_unstemmed | Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations |
| title_short | Whole Genome Sequencing and Re-sequencing of the Sable Antelope (Hippotragus niger): A Resource for Monitoring Diversity in ex Situ and in Situ Populations |
| title_sort | whole genome sequencing and re sequencing of the sable antelope hippotragus niger a resource for monitoring diversity in ex situ and in situ populations |
| topic | Hippotragus niger sable antelope genome assembly conservation genetics Bovidae |
| url | http://g3journal.org/lookup/doi/10.1534/g3.119.400084 |
| work_keys_str_mv | AT klauspeterkoepfli wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT gaiktamazian wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT davidwildt wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT paveldobrynin wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT changhoonkim wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT paulbfrandsen wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT raquelgodinho wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT andreyayurchenko wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT alekseykomissarov wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT kseniakrasheninnikova wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT sergeikliver wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT sofiakolchanova wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT margaridagoncalves wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT miguelcarneiro wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT pedrovazpinto wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT nunoferrand wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT jesusemaldonado wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT ginamferrie wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT leonachemnick wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT oliveraryder wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT warrenejohnson wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT pierrecomizzoli wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT stephenjobrien wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations AT budhanspukazhenthi wholegenomesequencingandresequencingofthesableantelopehippotragusnigeraresourceformonitoringdiversityinexsituandinsitupopulations |