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

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.