Integrated Transcriptomic and Proteomic Analyses Reveal Stage-Dependent Gill Remodeling Under Chronic Salinity Stress in Grass Carp (Ctenopharyngodon idella).

The expansion of brackish-water aquaculture for freshwater species such as grass carp (Ctenopharyngodon idella) necessitates a mechanistic understanding of their physiological and molecular responses to elevated salinity. Here, we performed integrated histopathological,transcriptomic and proteomic analyses of gill tissues from grass carp chronically exposed to 7‰ and 14‰ salinity to elucidate stage-specific responses to prolonged salinity stress. At moderate salinity (7‰), gill responses were characterized by epithelial stabilization, activation of adhesion-related pathways, enhanced carbohydrate metabolism, extracellular matrix (ECM) remodeling, and suppressed immune activity, accompanied by only mild histological alterations. In contrast, exposure to higher salinity (14‰) resulted in severe gill damage, including epithelial thickening, lamellar atrophy, vascular congestion, and hemorrhagic lesions, together with reduced survival. Multi-omics analyses revealed extensive immune, metabolic, and signaling reprogramming at 14‰, characterized by sustained immune suppression, intensified ECM remodeling, and a metabolic shift from carbohydrate utilization toward lipid- and sterol-associated pathways. Several candidates involved in apoptosis, epithelial maintenance, and sterol biosynthesis showed concordant regulation at both transcriptomic and proteomic levels. Collectively, these findings demonstrate a transition from acclimatory compensation at 7‰ to stress-associated tissue remodeling at 14‰. This study provides integrated multi-omics insights into salinity stress responses in grass carp and offers candidate pathways and genes for future studies on salinity tolerance mechanisms in freshwater aquaculture species.