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 Aden , Shaikha Salem Al Dhaheri, David Wildt, Shereen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden, Klaus-Peter Koepfli

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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
Original languageEnglish
Pages (from-to)1668-1681
JournalMolecular Ecology Resources
Issue number6
Early online date4 May 2020
Publication statusE-pub ahead of print - 4 May 2020


Dive into the research topics of 'Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild'. Together they form a unique fingerprint.

Cite this