Genome-wide identification and expression analysis of the Sox gene family in bivalves

Since the discovery of the Sox gene family in 1990, research on its distribution, classification, characterization, and function across various species has been significantly deepened. However, the Sox gene family has not yet been systematically and comprehensively analyzed in bivalves. In this study, 254 Sox genes were identified in 51 bivalves (covering 20 orders and 37 families). The Sox gene numbers ranged from 1 and 10 in most bivalves but no Sox gene was identified in the transcriptomes of Poromya illevis (Poromyoidea), Thracia phaseolina (Thracioidea), Solen vaginoides (Solenoidea), Lamychaena hians (Gastrochaenoidea), and Limopsis sp. and Solemya velesiana (Limopsoidea). The phylogenetic analyses revealed that Sox genes in bivalves are divided into 7 primary groups: SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, and SoxH, with different groups exhibiting distinct conserved motif patterns. Notably, SoxA and SoxG found in most vertebrates were not identified in bivalves. Moreover, through spatiotemporal expression profiling in 6 distinct bivalve species, it was determined that the SoxH genes exhibit male-biased expression mainly in non-hermaphroditic bivalves, while SoxB1 and SoxC genes demonstrate female-biased expression, and these two Sox genes may serve a pivotal role in embryonic development stage and SoxB2, SoxC and SoxE may play a significant impact in neural development in bivalves. Sox family members also appear to possess disparate functions across different species and tissues. Overall, this study may provide a basis for future investigations into the functions and evolution of Sox genes in bivalves, and offer new perspectives on their roles in development in bivalves.