Transcriptome analysis reveals physiological responses in liver tissues of Epinephelus cyanopodus under acute hypoxic stress

Dissolved oxygen (DO) in aquatic ecosystems plays a pivotal role in fish farming, serving as a critical determinant for the sustainable development of aquaculture practices. When fish suffer hypoxic stress, they undergo a cascade of physiological adaptations. In this study, healthy E. cyanopodus were subjected to experimental treatments under normoxic (6.0 ± 0.05 mg/L) and hypoxic (1.6 ± 0.05 mg/L) conditions for 1 (H1), 3 (H3), 6 (H6), and 9 (H9) h to evaluate physiological responses. Liver RNA-seq analysis identified 6152 differentially expressed genes (DEGs) between the control group (H0) and the four hypoxia-treated groups (H1, H3, H6, H9). RNA-seq results indicated that hypoxia for 3–6 h was the key duration when significant physiological changes occurred in E. cyanopodus . KEGG enrichment analysis revealed significant involvement of these DEGs in key hypoxia-responsive pathways, including HIF-1 signaling, Glutathione metabolism, p53 signaling, PPAR signaling, and PI3K-Akt signaling pathways. These DEGs primarily played function in biological processes, including glycolysis/gluconeogenesis ( aldob , hk , ldh-a , pparα , eno1 , gpt ), pyruvate metabolism ( aldocb , ldh-a , fabp1 ), immune response ( pnp , cxcl5 , tnf-α , il1-β , il12-β ), and apoptosis regulation ( bax , bcl2 , casp3 ). Their coordinated expression played a crucial role in mediating hypoxic adaptation of the liver and brain in E. cyanopodus . Three immune-related enzymes (AKP, ALT, AST), and two metabolic-related enzymes (GLU, LDH) were significantly expressed at 3 and 6 h. These results exactly proved that 3–6 h of hypoxic stress was the key period when E. cyanopodus experienced significant physiological changes. This study elucidated key physiological response changes underlying hypoxic stress in E. cyanopodus , which provided both theoretical framework for understanding hypoxic adaptation and practical insights for developing hypoxia-resistant breeding strategies.