Jensen Evelyn L, Marchisio Chiara, Ochoa Alexander, Gray Rachel, Parra Vanessa, Miller Joshua M, Çilingir F Gözde, Caccone Adalgisa
School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne UK.
Faculty of Health and Life Sciences Universitat Pompeu Fabra Barcelona Spain.
Ecol Evol. 2025 Apr 25;15(4):e71358. doi: 10.1002/ece3.71358. eCollection 2025 Apr.
The utility and importance of whole-genome sequences are recognized across various fields, including evolution and conservation. However, for some taxa, like extinct species, using methods to generate contiguous genomes that rely on high-quality DNA is impossible. In such cases, an alternative may be to employ synteny-based methods using a genome from a closely related taxon to generate more complete genomes. Here we update the reference genome for the Pinta Island Galapagos giant tortoise () without conducting additional sequencing through rescaffolding against the most closely related chromosome-level genome assembly, the Aldabra giant tortoise (). This effort resulted in a much more contiguous genome, CheloAbing_2.0, with an N50 that is two orders of magnitude longer and large reductions in L50 and the number of gaps. We then examined the impact of the CheloAbing_2.0 genome on estimates of runs of homozygosity (ROH) using genome resequencing data from 37 individual Galapagos giant tortoises from the 13 extant lineages to test the mechanisms by which a fragmented assembly may over- or underestimate the number and extent of ROH. The use of CheloAbing_2.0 resulted in individual estimates of inbreeding, including ROH proportion (F), number (N), and cumulative length (S), that were statistically different from those derived from the earlier genome assembly. This improved genome will serve as a resource for future efforts focusing on the ecology, evolution, and conservation of this species group. More broadly, our results highlight that synteny-based scaffolding is promising for generating contiguous genomes without needing additional data types.
全基因组序列的实用性和重要性在包括进化和保护在内的各个领域都得到了认可。然而，对于一些分类群，如已灭绝的物种，使用依赖高质量DNA来生成连续基因组的方法是不可能的。在这种情况下，一种替代方法可能是采用基于共线性的方法，利用来自密切相关分类群的基因组来生成更完整的基因组。在这里，我们通过与最密切相关的染色体水平基因组组装——阿尔达布拉巨型陆龟（Aldabra giant tortoise）进行重排支架，在不进行额外测序的情况下更新了平塔岛加拉帕戈斯巨型陆龟（Pinta Island Galapagos giant tortoise）的参考基因组。这项工作产生了一个更加连续的基因组CheloAbing_2.0，其N50长了两个数量级，L50和缺口数量大幅减少。然后，我们使用来自13个现存谱系的37只加拉帕戈斯巨型陆龟的基因组重测序数据，研究了CheloAbing_2.0基因组对纯合子连续片段（ROH）估计的影响，以测试片段化组装可能高估或低估ROH数量和范围的机制。使用CheloAbing_2.0得出的个体近亲繁殖估计值，包括ROH比例（F）、数量（N）和累积长度（S），与早期基因组组装得出的估计值在统计学上存在差异。这个改进的基因组将作为未来专注于该物种群生态、进化和保护工作的资源。更广泛地说，我们的结果突出表明，基于共线性的支架构建对于在不需要额外数据类型的情况下生成连续基因组很有前景。
