Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole‐genome sequences are currently available for three species. In this study, we have generated a chromosome‐level genome assembly of the fourth species, the Asian coastal horseshoe crab (Tachypleus gigas; genome size 2.0 Gb). The genome assembly has a scaffold N50 value of 140 Mb with ~97% of the assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas. In addition, we have generated the complete mitochondrial genome sequence and deep‐coverage transcriptome assemblies for four tissues. A total of 26,159 protein‐coding genes were predicted in the genome. The T. gigas genome contains five Hox clusters similar to the mangrove horseshoe crab (Carcinoscorpius rotundicauda), suggesting that the common ancestor of horseshoe crabs already possessed five Hox clusters. Phylogenomic and divergence time analysis suggested that the American and Asian horseshoe crab lineages shared a common ancestor around the Silurian period (~436 Ma). Comparison of the T. gigas genome with those of other horseshoe crab species with chromosome‐level assemblies provided insights into the chromosomal rearrangement events that occurred during the emergence of these species. The genomic resources of T. gigas will be useful for understanding their genetic diversity and population structure and would help in designing strategies for managing and conserving their stocks across Asia.

中文翻译：

---

沿海鲎 (Tachypleus gigas) 的染色体水平基因组组装。

仅由四种现存物种代表的马蹄蟹已经存在了大约 5 亿年。然而，由于人为活动，它们的存在现在正受到威胁。这些物种的基因组资源的可用性对于规划适当的保护措施很有价值。目前可用于三个物种的全基因组序列。在这项研究中，我们生成了第四个物种亚洲沿海鲎 ( Tachypleus gigas；基因组大小 2.0 Gb)的染色体水平基因组组装。基因组组装的支架 N50 值为 140 Mb，约 97% 的组装映射到 14 个支架，代表T. gigas 的14 条染色体. 此外，我们为四种组织生成了完整的线粒体基因组序列和深度覆盖转录组组装。在基因组中总共预测了 26,159 个蛋白质编码基因。在T.牡蛎基因组包含类似于圆尾鲎（5个Hox的簇Carcinoscorpius圆尾），表明马蹄蟹的共同祖先已经拥有5个Hox基因簇。系统发育和分化时间分析表明，美洲和亚洲马蹄蟹谱系在志留纪时期（~436 Ma）共享一个共同祖先。T. gigas 的比较与具有染色体水平组装的其他鲎物种的基因组的基因组分析提供了对这些物种出现期间发生的染色体重排事件的见解。T. gigas的基因组资源将有助于了解它们的遗传多样性和种群结构，并有助于设计管理和保护亚洲种群的策略。