Comparative transcriptomic profiling of gonads in Solea senegalensis: Exploring sex, maturity, and origin variations

Sex differentiation and determination are crucial processes in complex organisms, with fish exemplifying this diversity through various mechanisms. Solea senegalensis , a benthic flatfish significant for European aquaculture, faces reproductive challenges in captivity, particularly among captive-bred males. These challenges hinder genetic improvement efforts. Recently, the fshr gene was identified as responsible for sex determination in this species, but the pathways and genes involved in gonadal development remain unclear, as do the reproductive difficulties in hatchery-born individuals. This study aimed to analyze the gonadal transcriptome of mature and immature females and males, both wild and hatchery-born, grouped by sex, origin, and maturity for twelve comparative analyses. RNA was extracted and sequenced using Illumina technology, followed by differential expression analysis and GO and KEGG enrichment analyses. Results indicated that most differentially expressed genes were between sexes, with males showing more individual variation, followed by maturity stages and origin. The MAPK signaling pathway, particularly the p38 pathway, was significantly enriched, indicating its role in testicular development. Genes such as mapk11 , mapk12 , mapk13 , and mapk14 were overexpressed in males. In females, differential activation of canonical and non-canonical Wnt pathways highlighted their role in ovarian development. Genes associated with olfactory receptors were overexpressed in wild males compared to cultured (F1) males. These findings provide a clearer understanding of the genes involved in the gonadal development of S. senegalensis . • Differential expression in the gonad is primarily due to sex, not origin or maturity. • The MAPK signaling pathway is essential in male gonadal development. • Canonical and non-canonical Wnt pathways regulate female gonadal development. • Genes associated with olfactory receptors were overexpressed in wild males compared to cultured (F1) males.