Histological observation, transcriptome and methylome analyses reveal the dynamic changes during gonadal differentiation of spotted sea bass, Lateolabrax maculatus

The spotted sea bass ( Lateolabrax maculatus ) is a highly valuable species in Chinese aquaculture, yet its gonadal development remains poorly understood. This study employed histology, RNA-Seq, and whole genome bisulfite sequencing (WGBS) to investigate early gonadal differentiation. Histological analysis revealed that testicular differentiation commenced before 120 days post-hatching (dph), while ovarian differentiation appeared before 180 dph. Transcriptomic profiling at 90, 120, 180, and 250 dph identified male-biased DEGs (e.g., star , prom2 , igfbp2a , dmrt1 , gsdf ) and female-biased DEGs (e.g., slco4a1 , adma , prxl2a , foxl2 , id2 ), suggesting their involvement in testis and ovary formation, respectively. Thirty-one hub genes showed a sustained increase in expression during both testis and ovary differentiation, enriched in pathways such as ribosome biogenesis, RNA polymerase, spliceosome, and cytosolic DNA-sensing indicating roles in somatic and germ cell development. WGBS analysis at 180 dph showed that steroid hormone synthesis and transport pathways were associated with DNA methylation. Moreover, six genes ( acta1 , cacnb4 , crabp2 , dfna5 , app1 , and hoxb3a ) exhibited significant methylation differences between testes and ovaries, with expression levels negatively correlated with methylation. These genes may serve as key epigenetic targets during gonadal differentiation. Collectively, this study provides a comprehensive overview of transcriptional and epigenetic mechanisms driving early gonadal differentiation in spotted sea bass, offering new insights into sex differentiation in teleosts. • Histology revealed key testis and ovary differentiation stages at 120 and 180 dph in spotted sea bass, respectively. • Sex-biased DEGs, including dmrt1 , gsdf (male) and foxl2 , id2 (female), were identified during gonad differentiation. • 31 hub genes involved in ribosome biogenesis, RNA polymerase, and DNA-sensing pathways contribute to gonadal development. • Steroid hormone synthesis and transport genes were regulated by DNA methylation.