Chinese mitten crab, Eriocheir sinensis, is a high-economic-value aquatic crustacean in Chinese aquaculture, farmed in 28 provinces and municipalities nationwide, featuring large industry scale and profound cultural heritage. Due to the big number of chromosomes (2n=146), its genome shows high repetitive sequences and is difficult in assembly, and moreover, E. sinensis in different water systems shows rather distinctive environmental adaptability and biological characteristics. Meanwhile, broken limbs are much common to Chinese mitten crabs in production, which affects its industrial applicability and economic value.
Recently, Professor Wang Chenghui and his team from the College of Fisheries and Life Science, Shanghai Ocean University, in collaboration with Professor Li Chenhong, Professor Michael Hofreiter from the University of Potsdam, Germany, and Professor Lv Guoqing from the University of Nebraska at Omaha, USA, etc. used third-generation sequencing technology combined with BioNano optical mapping and Hi-C (high-throughput chromosome conformation capture) technology to sequence and assemble the whole genome of E. sinensis in the Yangtze River system, and obtained a fine genome map at the chromosome level. The assembled E. sinensis genome size was 1.67 Gb, covering 94.4% of its genome size (1.77 Gb), including 16.98 Mb for Scaffold N50 and 717.3 kb for Contig N50, and a total of 20286 protein-coding genes were identified.
E. sinensis is characterized in its unique limb regeneration, studying on which is of great research significance and industrial application value. In this study, comparative genomic analysis was conducted to identify genes and gene families unique to arthropods. The comparative transcriptome and gene co-expression analysis at different developmental stages of limb regeneration revealed that the Innexin gene family plays an important molecular signaling role in the early stage of limb regeneration in E. sinensis, in which the Innexin2 gene was specifically up-regulated within 1 day after limb amputation and mediated the limb regeneration process in E. sinensis by regulating the mTORC1 signaling pathway and the immune response.
In this study, it was also found that the early stage of limb regeneration in E. sinensis was regulated epigenetically, with the SMYDA gene family present only in arthropods and down-regulated at the early stage of broken limb in E. sinensis and restored to the level of expression at the time of no-broken limb. Further analysis revealed that this gene family was also differentially expressed throughout the metamorphosis process of E. sinensis from its megalopa larvae to crablet, suggesting that the arthropod-specific SMYDA gene family plays an important epigenetic modifying role in the biological processes of E. sinensis involving distinct morphogenesis such as metamorphosis and regeneration.
The study provides an important genomic resource and platform for conducting molecular breeding of E. sinensis, and provides useful guidance for improving farming production and management. The related results were published in Science Advances. Professor Wang Chenghui and Professor Li Chenhong from Shanghai Ocean University and Professor Michael Hofreiter from University of Potsdam, Germany are the corresponding authors of the paper, and Associate Professor Wang Jun and Dr. Chen Xiaowen from Shanghai Ocean University are the co-first authors. The study was funded by Shanghai Science and Technology-Based Key Agricultural Projects and Shanghai E. Sinensis Modern Agricultural Technology System Project.