Age- and tissue-dependent responses to Ichthyophthirius multifiliis in a schizothoracine fish

Ichthyophthirius multifiliis causes substantial loss in freshwater aquaculture, but molecular changes after treatment is poorly characterized in highland fishes. Following a natural I. multifiliis outbreak and standardized formalin treatment in Qinghai-Xizang Plateau endemic fish Schizopygopsis younghusbandi , we compared post-treatment fish in better condition with moribund fish (status) in juveniles and adults (age). Gill, head kidney, spleen, and intestinal tissues were collected for transcriptomic analysis, while intestinal contents were used for untargeted metabolomics. Using an age-by-status interaction, or delta, framework, we identified developmental and tissue-specific molecular differences between the two groups. Transcriptomic analysis identified 571 significant gene–tissue interaction effects representing 537 unique genes, with the strongest divergence in mucosal tissues (gill and intestine). Differences between the better-condition and moribund groups varied markedly between adults and juveniles and across tissues. Lipid metabolism emerged as the most prominent functional theme, although the direction of change differed among tissues. Tissue-specific co-expression analysis identified three modules with significant age by status interactions. Metabolomic analysis detected 191 interaction-associated features, while separate age-stratified KEGG analyses highlighted different candidate pathway profiles in adults and juveniles. Collectively, these findings reveal pronounced age- and tissue-dependent molecular heterogeneity between post-treatment clinical conditions. Our study provides molecular evidence supporting age-specific post-treatment management and highlights age-dependent immune and metabolic responses as key considerations for disease management in high-altitude endemic fishes.