Integrated transcriptomic analysis reveals potential ceRNA network and hub genes involved in sex determination and differentiation of the Pacific oyster (Crassostrea gigas)

Non-coding RNA (ncRNA) and competing endogenous RNA (ceRNA) network play vital roles in gene expression regulation, but their involvement in sex determination and differentiation remains unclear in molluscs. In this study, a comprehensive transcriptomic analysis was performed to investigate ncRNAs and ceRNA network in female and male gonads of Crassostrea gigas. Differential expression analysis identified 3496 mRNAs, 582 lncRNAs, 184 miRNAs, and 644 circRNAs with sex-biased expression. Functional enrichment analyses highlighted key pathways such as the cell cycle, oocyte meiosis, energy metabolism, and lipid metabolism, underscoring their involvement in sex determination and differentiation. A ceRNA network was constructed involving 398 lncRNAs, 119 circRNAs, 140 miRNAs, and 720 mRNAs. Hub genes, such as Fem1c, Spef1, Dgkq, Ppp1ca, Nkd1, Morn3, Dpf2, and Gabarap were identified, with pronounced sex-biased expression and localization in specific gonadal cell types, as revealed by bulk and single-nucleus RNA-seq analysis. These genes are associated with critical processes, including follicle development, spermatogenesis, and hormonal regulation. Collectively, these findings provide novel insights into the ceRNA-mediated regulatory mechanisms underlying sex determination and differentiation in C. gigas, contributing to a deeper understanding of molluscan reproductive biology.