Integrative Transcriptomic, Proteomic and Epigenetic Analysis Uncovers Reproductive Dysregulation in F1 Males of Solea senegalensis

Reproductive dysfunction in captive-bred males of the flatfish Solea senegalensis remains a major bottleneck for its aquaculture. To clarify the molecular basis underlying these impairments, we performed an integrated analysis of transcriptomes, proteomes and methylomes from gonads of wild-type individuals and first-generation (F1) captive fish of both sexes. Nineteen RNA-seq libraries and eighteen LC–MS/MS proteomes were generated, allowing the quantification of more than 32,000 genes and 2221 proteins. Differential expression and principal component analyses revealed that sex was the primary driver of molecular variation, whereas origin (F1 vs. wild-type) had a more moderate effect. Multi-omics integration showed a partial and comparison-dependent correspondence between RNA and protein levels, with a marked RNA–protein decoupling in F1 males. Despite this limited concordance, functional enrichment analyses identified consistent regulation of key biological processes, including translation, energy metabolism, and reproductive pathways such as gametogenesis, fertilization, and early embryonic development. Within this regulatory framework, previously characterized DNA methylation landscapes in gonadal tissue suggest an additional epigenetic layer modulating the transcriptional potential of reproductive genes, particularly in captive-bred males. F1 males exhibited coordinated down-regulation of reproductive functions across omic layers, consistent with altered post-transcriptional and post-translational regulation. Overall, this study provides the first comprehensive multi-omics framework integrating transcriptomic, proteomic, and epigenetic information in S. senegalensis gonads, offering mechanistic insights into the molecular basis of reproductive dysfunction in F1 broodstock and supporting future strategies to improve reproductive performance in aquaculture.