The Chinese mitten crab (Eriocheir sinensis) is widely distributed along eastern China, where northern and southern populations may have evolved different environmental adaptation mechanisms. DNA methylation, as an important epigenetic modification, plays a key regulatory role in environmental adaptation. In this study, muscle and hepatopancreas tissues from E. sinensis populations of the Liaohe River (LH) and Beilunhe River (BLH) were subjected to integrated RNA-seq and whole-genome bisulfite sequencing (WGBS) analyses, generating 12 mRNA libraries and 12 DNA methylation libraries. RNA-seq analysis identified 622 and 783 differentially expressed genes (DEGs) in muscle and the hepatopancreas, respectively, in the LH group compared with the BLH group, with downregulated genes accounting for a larger proportion. WGBS analysis showed that genome-wide DNA methylation in E. sinensis was predominantly in the CG context, with the highest methylation levels observed in gene body regions. A total of 972 and 991 differentially methylated regions (DMRs) were identified in muscle and the hepatopancreas, respectively. Integrated analysis further identified 10 differentially methylated and expressed genes (DMEGs) in muscle and 26 DMEGs in the hepatopancreas. Notably, no single fixed pattern was observed between methylation changes and gene expression changes in either tissue. These findings suggest that DNA methylation may participate in environmental adaptation in northern and southern populations of E. sinensis by modulating gene expression. Our results highlight the important role of epigenetic regulation in the evolutionary adaptation of crustaceans to different environments and provide a theoretical basis for the development of environment-associated molecular markers and the evaluation of adaptive germplasm resources.

Chinese mitten crab (Eriocheir Sinensis) is a commercially important species in Chinese aquaculture, yet the genetic structure of wild populations remains poorly understood. A total of 240 wild E. sinensis samples were collected from Liaohe (LH), Yalujiang (YLJ), Huanghe (HH), Yangtze (including Anqing section (YZA), Taixing section (YZT)), Oujiang (OJ), Minjiang (MJ), and Beilunhe (BLH) River basins to investigate the genetic structure of native populations. Through genotyping-by-sequencing (GBS) and stringent quality filtering, a total of 3,120,408 high-quality single- nucleotide polymorphism (SNP) loci were identified. Principal component analysis (PCA) showed that the BLH and MJ populations formed distinct clusters, whereas OJ, YZA, YZT, HH, LH, and YLJ populations were loosely clustered. Phylogenetic tree and population genetic structure analyses revealed that the BLH River population in southern China was the only significantly differentiated group within the native range of the Chinese mitten crab, while northern populations (HH, LH, and YLJ) exhibited stronger admixture, indicating higher levels of gene flow. Additionally, gene flow occurred more frequently among geographically proximate populations, while weaker gene flow persisted between geographically distant groups. Further selective sweep analyses comparing representative southern and northern populations (BLH and LH) identified key genes under strong geographic selection, primarily involved in transcriptional regulation, metabolism and transport, stress response and damage repair, and signal transduction. Overall, this study provides comprehensive insights into the genetic resources of wild E. sinensis across Chinese river basins, laying a foundation for conservation and germplasm resource development.