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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

Citation

Humble, Emily et al. (2020), Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild, Dryad, Dataset, https://doi.org/10.5061/dryad.qbzkh18f7

Abstract

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.

Methods

Here we used whole genome resequencing data together with a chromosomal-level genome assembly to investigate diversity and demography in the scimitar-horned oryx, an extinct in the wild antelope. Illumina sequencing was carried out for six focal individuals at an average coverage of 15X. Raw sequencing reads were processed and mapped to the genome assembly for downstream analysis. This repository contains metadata and some processed files that should make it possible to reproduce our analyses using code available on github. Raw sequencing reads are stored in the European Nucleotide Archive (ENA) under study accession PRJEB37295. More information can be found in the README file.

Usage Notes

Repositories containing the full analysis code can be found here: https://github.com/elhumble/SHO_reseq_2020 and here: https://github.com/elhumble/SHO_analysis_2020. The README file and comments in scripts should contain all relevant information to reproduce the downstream analyses in the paper.

Funding

Welch Foundation, Award: Q‐1866