Gonadal Transcriptome Differences Between the Sexes in Wild Caught Southern Flounder ( Paralichthys lethostigma) During a Critical Development Period

Flounder in the genus Paralichthys exhibit a unique sex determination system that combines genotypic and temperature-dependent mechanisms. In southern flounder ( Paralichthys lethostigma ), XY individuals develop as males, while XX individuals’ sex is influenced by juvenile developmental temperatures. Little is known about the genes involved in this process. This study uses pooled RNA sequencing to create a de novo gonadal transcriptome and identify genes related to sex determination and differentiation in wild-caught juvenile southern flounder from two North Carolina locations with differing sex ratios. The transcriptome assembly revealed 68,331 uniquely annotated genes with high functional specificity. Nine genes were linked to sex determination, including five novel to southern flounder and associated with epigenetic mechanisms like m6a methylation and alternative splicing, suggesting epigenetic influence in male development. Additionally, genes in the TGF-β signaling pathway were differentially expressed, supporting this pathway’s role in sex differentiation. This study provides a valuable transcriptome resource for future research on southern flounder.