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Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

View ORCID ProfileEmily Humble, View ORCID ProfilePavel Dobrynin, View ORCID ProfileHelen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, View ORCID ProfileOlga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, David Wildt, Shireen Oliaji, View ORCID ProfileGaik Tamazian, View ORCID ProfileBudhan Pukazhenthi, View ORCID ProfileRob Ogden, View ORCID ProfileKlaus-Peter Koepfli
doi: https://doi.org/10.1101/867341
Emily Humble
1Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, UK
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  • For correspondence: emily.humble@ed.ac.uk
Pavel Dobrynin
2Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, Virginia 22630 and Washington, D.C. 20008 USA
3Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199034, Russian Federation
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Helen Senn
4RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
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Justin Chuven
5Terrestrial & Marine Biodiversity, Environment Agency – Abu Dhabi, United Arab Emirates
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Alan F. Scott
6Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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David W. Mohr
6Genetic Resources Core Facility, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Olga Dudchenko
7The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
8Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
9Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA
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Arina D. Omer
7The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
8Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
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Zane Colaric
7The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
8Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
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Erez Lieberman Aiden
7The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
8Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
9Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA
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David Wildt
2Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, Virginia 22630 and Washington, D.C. 20008 USA
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Shireen Oliaji
1Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, UK
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Gaik Tamazian
10Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russian Federation
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Budhan Pukazhenthi
2Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, Virginia 22630 and Washington, D.C. 20008 USA
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Rob Ogden
1Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, UK
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Klaus-Peter Koepfli
2Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, Virginia 22630 and Washington, D.C. 20008 USA
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Abstract

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

Footnotes

  • ↵* Recognised as joint senior authors

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild
Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden, Klaus-Peter Koepfli
bioRxiv 867341; doi: https://doi.org/10.1101/867341
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Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild
Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden, Klaus-Peter Koepfli
bioRxiv 867341; doi: https://doi.org/10.1101/867341

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