Gill methylome and transcriptome patterns in the context of freshwater intolerance in European sea bass

Epigenetic marks induced by the environment play a key role in phenotypic plasticity and stress tolerance. We examined phenotypic responses in European sea bass D. labrax following a two-week exposure to fresh water (FW). FW transfer resulted in two distinct tolerance phenotypes: a tolerant (FWt) and an intolerant (FWi) group. FWi showed severe ion imbalance and pronounced stress. Using a genome-wide approach, we compared gill transcriptomic and DNA methylation profiles between phenotypes. RNA-seq analysis identified 7953 differentially expressed genes. Although ion transport pathways were not significantly altered, FWi showed profoundly modulated expression of genes involved in protein synthesis and quality control. These changes were associated with enhanced metabolic and biosynthetic processes, likely reflecting active gill remodelling under osmotic stress. In contrast, genes involved in tissue integrity, epithelial barrier function, and cell adhesion were downregulated. DNA methylation analysis revealed 5320 differentially methylated regions (DMRs) between phenotypes, with over 80% hypomethylated in FWi, suggestive of accelerated biological aging. Hypomethylation in promoters and first exons/introns was mainly linked to genes involved in cell structure and cell-cell interactions. Concordant hypomethylation and upregulation were observed for genes involved in the sphingolipid pathway, cytoskeleton organization, and cell signalling. Downregulated, hypermethylated genes were associated with GTPase activity and immune defence. Overall, our results exclude gill dysfunction as the cause of osmoregulatory failure. However, they also suggest that FW exposure may accelerate aging and reduce lifespan in FWi, potentially due to reduced plasticity and/or genetic variability. • Freshwater exposure reveals tolerant and intolerant phenotypes in D. labrax . • Intolerant fish show ion imbalance and strong stress response. • Gill transcriptome changes reflect remodelling, not osmoregulatory failure. • Intolerant phenotype shows widespread DNA hypomethylation in gills. • Freshwater stress may accelerate biological aging and reduce lifespan.