Deciphering the genetic basis of sex differentiation in silver-lipped pearl oyster ( ) based on integrative transcriptomic analysis.

The silver-lipped pearl oyster ( ) is the largest and most commercially valuable pearl-producing oyster, renowned for its ability to generate large, lustrous pearls. This species is a sequential hermaphrodite, with pearl production displaying notable sexual dimorphism. Consequently, understanding the molecular mechanisms governing sex determination and differentiation is crucial for advancing breeding strategies in the pearl oyster industry. To elucidate these mechanisms, this study conducted integrative transcriptomic analyses of gonadal tissues using isoform sequencing (Iso-seq) and RNA sequencing (RNA-seq). Comparative analysis of ovarian and testicular tissues identified 2 768 differentially expressed genes (DEGs). Gene co-expression network analysis delineated four key modules, including three sex-specific modules and one shared module. Key genes implicated in sex determination and maintenance were identified, including , , and , important for ovarian maintenance, and , , , and , crucial for testicular maintenance. These genes, widely studied in other taxa, were confirmed as hub genes in the sex-related modules of . Interestingly, genes within the shared module were significantly enriched in the spliceosome pathway. Alternative splicing analysis highlighted its extensive role in gonadal tissues, with more pronounced activity observed in the testis compared to the ovary. Nearly half (47.83%, 375) of the identified genes undergoing differential alternative splicing (DASGs) also exhibited differential transcript usage (DTUGs), while only 17% of DTUGs overlapped with DEGs. Genes associated with sex differentiation, such as , , and , displayed sex-specific and/or sex-biased isoforms. These findings offer novel insights into the molecular basis of sex differentiation in , which could inform the development of targeted breeding strategies aimed at sex control, thereby enhancing pearl quality and yield in aquaculture. This study offers a robust molecular foundation for advancing breeding programs and optimizing production in the pearl oyster industry.