Lan Linjing, Zhang Xin, Yang Shanxiu, Mao Xiuguang, Dong Ji
School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou 510799, China.
J Hered. 2025 Jul 21;116(4):499-512. doi: 10.1093/jhered/esae077.
A high-quality reference genome is quite valuable in assessing the conservation status of a rare species when adequate data from other sources are unavailable. Bats comprise almost a fifth of all mammals and contribute greatly to the ecosystem. However, due to the nocturnal and elusive habits, it is difficult to obtain the accurate census population size of a rare bat species and assess its conservation status. Here, we generate a chromosome-level genome assembly for the king horseshoe bat (Rhinolophus rex) and assess its conservation status by comparing the genome-wide summary statistics with other related species. The genome assembly size was 2.1 Gb (contig N50: 75.26 Mb) and 99.9% of the total sequences were anchored onto 30 autosomes, X and Y chromosomes. Despite lower genome-wide heterozygosity and recent inbreeding, R. rex did not exhibit a higher genetic load compared with the other two Rhinolophus species. Historical demography analysis revealed that R. rex maintained a long-term (2 million years) stable population size (150,000). In the future, whole-genome sequencing data from more individuals will be needed to comprehensively assess the conservation status at recent timescales. We also reconstructed the ancestral karyotype of Rhinolophus as 2n = 54 and found that Robertsonian fissions and fusions were the main mechanisms of chromosomal rearrangements in this genus. Overall, our study shows important implications of reference-quality genomes in both conservation genomics and comparative genomics.
当无法从其他来源获得足够数据时，高质量的参考基因组对于评估珍稀物种的保护状况非常有价值。蝙蝠几乎占所有哺乳动物的五分之一，对生态系统有很大贡献。然而，由于蝙蝠具有夜行性且难以捉摸的习性，很难获得珍稀蝙蝠物种准确的普查种群数量并评估其保护状况。在这里，我们为大足鼠耳蝠（Rhinolophus rex）生成了一个染色体水平的基因组组装，并通过将全基因组汇总统计数据与其他相关物种进行比较来评估其保护状况。基因组组装大小为2.1 Gb（重叠群N50：75.26 Mb），99.9%的总序列被锚定到30条常染色体、X和Y染色体上。尽管全基因组杂合度较低且近期存在近亲繁殖，但与其他两种菊头蝠属物种相比，大足鼠耳蝠并未表现出更高的遗传负荷。历史种群动态分析表明，大足鼠耳蝠维持了长期（约200万年）稳定的种群数量（约15万）。未来，需要更多个体的全基因组测序数据来全面评估近期时间尺度上的保护状况。我们还重建了菊头蝠属的祖先核型为2n = 54，并发现罗伯逊易位和融合是该属染色体重排的主要机制。总体而言，我们的研究表明参考质量的基因组在保护基因组学和比较基因组学中都具有重要意义。
