Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.
Genomics Proteomics Bioinformatics. 2020 Aug;18(4):443-454. doi: 10.1016/j.gpb.2019.01.006. Epub 2020 Dec 18.
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）是甲壳动物中一种重要的水产养殖物种。尽管功能分析至关重要，但由于缺乏足够的基因组或转录组资源，其分析一直受到阻碍。在这项研究中，对 59 个样本进行了转录组测序，这些样本代表了不同的发育阶段（受精卵、幼体、大眼幼体、三个幼虫亚阶段、幼蟹和成年蟹）和不同的组织（幼蟹的眼柄、肝胰腺和肌肉，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 19023 个编码蛋白的基因。基于 128 个差异表达的表皮相关基因的层次聚类揭示了早期幼体发育阶段的两种截然不同的表达模式，表明这些基因在变态过程中的“蟹状”表皮形成和蜕皮后的表皮钙化中发挥着不同的作用。从 7 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了这样一种假设，即软甲纲和鳃足纲不形成单系群。此外，鳃足纲在系统发育上与六足纲更为密切相关，六足纲和鳃足纲的分支与软甲纲属于泛甲壳类。本研究为中华绒螯蟹提供了高质量的转录组资源，并展示了主要节肢动物类群的进化关系。本研究中鉴定的差异表达基因有助于进一步研究表皮相关基因表达网络，这些基因可能与变态过程中的“蟹状”表皮形成和蜕皮后的表皮钙化有关。
