Comparative analysis of differential gene expression in hepatopancreas of Chinese mitten crabs (Eriocheir sinensis) with different carapace colors

Abstract

The carapace color of the Chinese mitten crab (Eriocheir sinensis) significantly influences consumer preference and market value, yet the underlying molecular mechanisms remain poorly understood. In this study, transcriptome sequencing coupled with weighted gene co-expression network analysis (WGCNA) was employed to elucidate genetic and metabolic pathways involved in three genetically distinct carapace color phenotypes (red, white, and green). Hepatopancreatic transcriptome analyses across these color variants identified 910, 1555, and 1598 differentially expressed genes (DEGs) in pairwise comparisons. Functional enrichment analyses revealed significant activation of oxidoreductase activity, retinol metabolism, and mitochondrial energy metabolism pathways in crabs with red carapaces. Notably, key pigmentation-associated genes, including ninaB (carotenoid isomerase) and sno1 (flavin monooxygenase), were markedly upregulated. Additionally, WGCNA identified a highly correlated (r = 0.97) red-specific gene module enriched predominantly with oxidative phosphorylation-related genes, such as atpsycf6 and ndufb4, emphasizing the energetic investment associated with pigment biosynthesis. Furthermore, retinol metabolism emerged as a pivotal pathway connecting carotenoid processes with immune and antioxidant functions, implying potential physiological trade-offs between pigmentation and stress resilience. Overall, this study advances our understanding of crustacean carapace coloration mechanisms and provides valuable genetic targets for selective breeding aimed at enhancing desirable color traits in E. sinensis.