Comprehensive identification and expression profiling of piRNA pathway genes in the Pacific oyster Crassostrea gigas

PIWI-interacting RNAs (piRNAs) and their associated proteins are key regulators of germline development and genome defense, but their roles in mollusks remain largely unexplored. In this study, we systematically identified 28 piRNA pathway genes in the Pacific oyster Crassostrea gigas and characterized their genomic composition and expression profiles. The oyster piRNA gene repertoire exhibits a mosaic-like architecture, combining deeply conserved components with lineage-specific features, including the presence of vertebrate-type transcription factors such as A-MYB, the absence of the insect-specific RDC complex, and the retention of the exonuclease MUT7, which has been lost in several vertebrate and insect lineages. Transcriptome analyses revealed pronounced tissue-, stage-, and sex-biased expression patterns, consistent with this composite regulatory configuration. Several key factors, including CgPiwil1, CgGtsf1, and CgTdrd5 exhibit female-biased expression peaking at the maturation stage of the gonads, whereas CgYthdc2, CgMyb, and CgHsp83 show preferential expression in male gonads. Furthermore, CgHsp83 displays high expression in gills, suggesting potential multifunctional roles beyond germline regulation. qPCR validation of representative genes confirmed the transcriptome-based patterns. These findings provide the first comprehensive overview of the piRNA pathway in mollusks, reveal both conserved and divergent features compared to model animals, and establish a foundation for future functional studies on germline regulation in bivalves.