Transcriptomic and metabolomic analysis of metabolite changes and regulatory mechanisms associated with gonadal degeneration in yellow oil crab (Scylla paramamosain)

The yellow oil crab is a highly valuable aquatic species, with the accumulation of nutritional and flavor compounds closely linked to the degree of gonadal degeneration. However, the molecular mechanisms of gonadal degeneration remain unclear. In this study, we analyzed the differences in gene expression and metabolite accumulation across three gonadal degeneration stages (QX, GX, and TSX) in yellow oil crab using transcriptome and non-targeted metabolomics approaches, and identified key genes and metabolites involved. A total of 240 differential accumulated metabolites (DAMs) were identified, most of which were significantly more highly accumulated in GX and TSX than in QX. K-means clustering analysis of DAMs and gene expression data revealed distinct stage-specific expression patterns from QX to TSX stage. Moreover, the “steroid hormone biosynthesis” pathway was significantly enriched, with 15 highly expressed steroid hormones and their derivatives in GX and TSX. 7 types of key genes involved in steroid hormone biosynthesis (such as UGT, HSD17B12, STS, HSD3B, SULT1E1, SRD5A1, and CYP1A1) showed a trend of upregulation in GX and TSX stages. Gene-metabolite regulatory network analysis revealed significant correlations between 14 steroid hormones and 13 structural genes related to their biosynthesis (|r| > 0.8, p < 0.05). Therefore, the identified differential steroid hormones and seven key genes were positively associated with gonadal degeneration in yellow oil crab. These results offer a theoretical basis for understanding the formation and aquaculture of the yellow oil crab.