Research output: Contribution to journal › Article › peer-review
Chromosomal-level genome assembly of the scimitar-horned oryx : Insights into diversity and demography of a species extinct in the wild. / Humble, Emily; Dobrynin, Pavel; Senn, Helen; Chuven, Justin; Scott, Alan F.; Mohr, David W.; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Lieberman Aiden, Erez; Al Dhaheri, Shaikha Salem; Wildt, David; Oliaji, Shireen; Tamazian, Gaik; Pukazhenthi, Budhan; Ogden, Rob; Koepfli, Klaus Peter.
In: Molecular Ecology Resources, Vol. 20, No. 6, 01.11.2020, p. 1668-1681.Research output: Contribution to journal › Article › peer-review
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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 - Publisher Copyright: © 2020 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.
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 - conservation genomics
KW - Hi-C
KW - PSMC
KW - single nucleotide polymorphism (SNP)
KW - whole genome resequencing
KW - POPULATION
KW - WHOLE-GENOME
KW - COMPLETENESS
KW - POLYMORPHISM
KW - INFERENCE
KW - HETEROZYGOSITY
KW - GENETIC DIVERSITY
KW - CONSERVATION
KW - SEQUENCE
KW - HISTORY
UR - http://www.scopus.com/inward/record.url?scp=85085919839&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/54326150-f94c-311d-8b43-73c8f55e9eed/
U2 - 10.1111/1755-0998.13181
DO - 10.1111/1755-0998.13181
M3 - Article
AN - SCOPUS:85085919839
VL - 20
SP - 1668
EP - 1681
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
SN - 1755-098X
IS - 6
ER -
ID: 70122881