TY - JOUR
T1 - Chromosomal-level genome assembly of the scimitar-horned oryx
T2 - Insights into diversity and demography of a species extinct in the wild
AU - Humble, Emily
AU - Dobrynin, Pavel
AU - Senn, Helen
AU - Chuven, Justin
AU - Scott, Alan F.
AU - Mohr, David W.
AU - Dudchenko, Olga
AU - Omer, Arina D.
AU - Colaric, Zane
AU - Lieberman Aiden, Erez
AU - Al Dhaheri, Shaikha Salem
AU - Wildt, David
AU - Oliaji, Shireen
AU - Tamazian, Gaik
AU - Pukazhenthi, Budhan
AU - Ogden, Rob
AU - Koepfli, Klaus Peter
N1 - Funding Information:
We dedicate this paper with great fondness to our coauthor, Dr David Wildt, who passed away in January 2020. We are grateful for the encouragement, enthusiasm and wisdom that he provided during this research, which is a testament to the many important contributions he made to conservation science of endangered species during his career. We would like to thank the EAD and all EAZA and AZA SSP institutions that provided samples for this study. We would like to acknowledge Tania Gilbert at Marwell Wildlife for advice and for access to the international studbook. We would also like to thank Jack Humble for generating the chromosome rearrangement figure using D3.js. ELA was supported by an NSF Physics Frontiers Center Award (PHY1427654), the Welch Foundation (Q‐1866), a USDA Agriculture and Food Research Initiative Grant (2017‐05741), an NIH 4D Nucleome Grant (U01HL130010), and an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375). Whole‐genome resequencing was carried out by Edinburgh Genomics. Funding for reference genome sequencing was provided by the Smithsonian Institute and the Sichel Endowment Fund.
Publisher Copyright:
© 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
PY - 2020/11/1
Y1 - 2020/11/1
N2 - 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. 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 large-scale and 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.
AB - 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. 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 large-scale and 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.
KW - 10X Chromium
KW - Hi-C
KW - PSMC
KW - conservation genomics
KW - single nucleotide polymorphism (SNP)
KW - whole genome resequencing
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U2 - 10.1111/1755-0998.13181
DO - 10.1111/1755-0998.13181
M3 - Article
C2 - 32365406
AN - SCOPUS:85085919839
SN - 1755-098X
VL - 20
SP - 1668
EP - 1681
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 6
ER -