Multi-omics analysis provides new insights into the adaptive strategies of Procambarus clarkii in response to acute hypoxia stress

Suitable dissolved oxygen levels are crucial for crustacean respiration and energy metabolism. To investigate the molecular mechanisms underlying hypoxia adaptation in the red swamp crayfish ( Procambarus clarkii ), we performed an integrated multi-omics analysis combining RNA-Seq transcriptomics and LC-MS non-targeted metabolomics on gill tissues under acute hypoxic (2.0±0.2 mg/L) and normoxic (7.5±0.2 mg/L) conditions. A total of 1,021 differentially expressed genes (DEGs) and 286 differentially expressed metabolites (DEMs) were identified. KEGG enrichment analysis revealed that DEGs were predominantly associated with lipid metabolism pathways, whereas DEMs were significantly enriched in nucleotide metabolism, purine metabolism, ABC transporter pathways and unsaturated fatty acid biosynthesis. Integrated transcriptomic and metabolomic analysis revealed 47 genes and 47 metabolites significantly associated across multiple key metabolic pathways, including lipid, carbohydrate, amino acid, and nucleotide metabolism. Specifically, genes associated with lipid synthesis and lipid degradation were upregulated, while the pentose phosphate pathway was activated to provide raw materials for fatty acid synthesis and produce NADPH to defend cell membranes from oxidative stress damage, indicating significant adjustments in energy metabolism pathways under hypoxic conditions. These findings provide a theoretical basis for deepening our understanding of hypoxic adaptation strategies in crustaceans. This multi-omics integration systematically revealed a coordinated metabolic reprogramming strategy in the gills of P. clarkii under acute hypoxia. These findings highlight the shift toward enhanced lipid turnover and NADPH production pathways (e.g., the pentose phosphate pathway) as key adaptive mechanisms, providing new insights into energy homeostasis and hypoxia tolerance in crustaceans beyond the traditional glycolysis-centered model.