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.

中文翻译：

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弯角羚羊的染色体水平基因组组装：深入了解野生灭绝物种的多样性和人口统计学。

圈养种群为防止野外灭绝提供了宝贵的保障。然而，它们也容易受到近亲繁殖、选择和漂变的负面影响。因此，遗传信息被认为是保护管理的一个重要方面。测序技术的最新发展有可能改善管理计划的成果；然而，这些方法向应用保护的转变进展缓慢。弯角羚羊 ( Oryx dammah)是一种北非羚羊，自 20 世纪 80 年代初以来在野外已经灭绝，是大规模、长期重新引入项目的重点。为了选择合适的创始人个体、促进放归后监测并改善圈养繁殖管理，需要全面的基因组资源。在这里，我们使用 10X Chromium 测序和 Hi-C 接触图谱来开发该物种的染色体水平基因组组装。所得组装包含 29 条染色体，支架 N50 为 100.4 Mb，并与牛基因组表现出强烈的染色体同线性。利用另外六个个体的重测序数据，我们证明了弯角羚羊与其他哺乳动物相比具有相对较高的遗传多样性，尽管它在圈养中经历了强烈的创始事件。此外，不同人群的多样性水平根据管理策略的不同而有所不同。最后，我们发现了与更新世气候变化时期相一致的动态人口历史。总的来说，我们的研究提供了一个清晰的例子，说明基因组数据如何能够揭示圈养种群的宝贵见解，并为指导濒危物种的未来管理决策提供重要资源。