Horseshoe crabs are marine chelicerates that have existed on Earth for about 450 million years, and they are often used as an experimental model for studying marine invertebrate embryology. In this study, we performed transcriptome gene expression profiling of four continuous embryonic stages (Stages 18–21) and first instar larvae of Tachypleus tridentatus. A mean of 50,742,995 high-quality clean reads was obtained from each library. We then conducted weighted gene co-expression network analysis (WGCNA) for 13,698 genes with fragments per kilobase of exon per million mapped fragments values >5. We identified 17 modules, six of which likely play critical roles in development. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes was performed on the biologically significant modules. We found that several pathways, such as hedgehog signaling pathway, VEGF signaling pathway, dorso-ventral axis formation, may be involved in the embryonic development process of T. tridentatus. We also identified hub genes that were highly connected in the six critical modules. This is the first study to apply WGCNA to horseshoe crabs to identify hub genes that may play critical roles in development, and our results provide new insight into the mechanisms underlying early development in horseshoe crabs.

马蹄蟹是一种海洋螯虾，在地球上已经存在了大约 4.5 亿年，它们经常被用作研究海洋无脊椎动物胚胎学的实验模型。在这项研究中，我们进行了四个连续胚胎阶段（第 18-21 阶段）和三齿鲎第一龄幼虫的转录组基因表达谱分析。. 从每个文库中平均获得了 50,742,995 条高质量的干净读数。然后，我们对 13,698 个基因进行加权基因共表达网络分析 (WGCNA)，其中每千碱基外显子每百万映射片段值 > 5 的片段。我们确定了 17 个模块，其中 6 个可能在开发中发挥关键作用。对具有生物学意义的模块进行差异表达基因的京都基因百科全书和基因组通路富集分析。我们发现刺猬信号通路、血管内皮生长因子信号通路、背腹轴形成等多种途径可能参与了三齿虎的胚胎发育过程。. 我们还确定了在六个关键模块中高度连接的枢纽基因。这是第一项将 WGCNA 应用于鲎以鉴定可能在发育中发挥关键作用的枢纽基因的研究，我们的研究结果为鲎早期发育的机制提供了新的见解。