PT  - JOURNAL ARTICLE
AU  - Emily Humble
AU  - Pavel Dobrynin
AU  - Helen Senn
AU  - Justin Chuven
AU  - Alan F. Scott
AU  - David W. Mohr
AU  - Olga Dudchenko
AU  - Arina D. Omer
AU  - Zane Colaric
AU  - Erez Lieberman Aiden
AU  - David Wildt
AU  - Shireen Oliaji
AU  - Gaik Tamazian
AU  - Budhan Pukazhenthi
AU  - Rob Ogden
AU  - Klaus-Peter Koepfli
TI  - Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild
AID  - 10.1101/867341
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 867341
4099  - http://biorxiv.org/content/early/2019/12/08/867341.short
4100  - http://biorxiv.org/content/early/2019/12/08/867341.full
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 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.