Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting.

中华绒螯蟹（Eriocheir sinensis）是甲壳纲重要的水产养殖品种。功能分析虽然必不可少，但由于缺乏足够的基因组或转录组资源而受到阻碍。在这项研究中，对 59 个代表不同发育阶段（受精卵、zoea、megalopa、幼虫、幼蟹和成蟹的三个亚阶段）​​和不同组织（眼柄、肝胰腺和幼蟹肌肉）的样本进行了转录组测序。 ，以及成年蟹的眼柄、肝胰腺、肌肉、心脏、胃、鳃、胸神经节、肠、卵巢和睾丸）。. 组装了一个全面的参考转录组，包括 19,023 个蛋白质编码基因。基于 128 个差异表达的角质层相关基因的分层聚类揭示了幼虫早期发育阶段两种不同的表达模式，证明了这些基因在变态过程中的“蟹状”角质层形成和蜕皮后角质层钙化中的不同作用。从七种节肢动物和秀丽隐杆线虫中鉴定的 1406 个一对一直系同源基因家族的系统发育分析强烈支持 Malacostraca 和 Branchiopoda 不形成单系群的假设。此外，鳃足纲与六足纲在系统发育上的亲缘关系更为密切，六足纲和鳃足纲的进化枝和马拉科斯特拉科的进化枝都属于Pancrustacea。本研究为E. sinensis提供了高质量的转录组资源，并展示了主要节肢动物群的进化关系。本研究中鉴定的差异表达基因促进了对角质层相关基因表达网络的进一步研究，这些基因表达网络可能与蜕皮后的变态和角质层钙化过程中的“蟹状”角质层形成有关。