Aden , Erez Lieberman

Al Dhaheri, Shaikha Salem

Chuven , Justin

Colaric , Zane

Dobrynin, Pavel

Dudchenko , Olga

Humble, Emily

Koepfli, Klaus-Peter

Mohr , David W.

Ogden, Rob

Oliaji, Shereen

Omer, Arina D.

Pukazhenthi, Budhan

Scott , Alan F.

Senn, Helen

Tamazian, Gaik

Wildt, David

English

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 thefocus 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 dynamicdemographic 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 endangeredspecies.<br/

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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

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https://www.research.ed.ac.uk/files/185099948/1755_0998.13181.pdf

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

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