Effects of High-Flow-Velocity Stress on Energy Metabolism and Transcription Level of Triplophysa orientalis

River channel development and hydraulic engineering alter natural flow-velocity patterns, subjecting <i>Triplophysa orientalis</i> to heightened hydrodynamic stress and energy expenditure in high-flow-velocity habitats. Regulating the molecular regulatory mechanisms underlying their adaptation to high-flow velocities provides a basis for species conservation and habitat optimization. Fish were exposed for 3 days to a normal flow velocity (3 BL/s) or a high flow velocity (33 BL/s) in a controlled circular swimming system that maintained a stable current without a deliberate low-flow velocity refuge; fish at 33 BL/s sustained upstream swimming throughout the exposure. RNA-seq differential expression analysis and GO/KEGG enrichment were performed on harvested skeletal muscle, with key genes validated via qPCR. A total of 78 differentially expressed genes (DEGs) were identified between the high-flow-velocity group and the normal-flow-velocity group, including 55 up-regulated genes and 23 down-regulated genes. GO and KEGG analyses revealed that the DEGs were predominantly enriched in mitochondrial energy metabolism and neural regulation, notably oxidative phosphorylation, and were further linked to FoxO and IL-17 signaling. Compared to the normal-flow-velocity group, the high-flow-velocity group exhibited significant down-regulation of multiple oxidative phosphorylation-related subunits, including <i>Mt-co1</i>, <i>Mt-co2</i>, <i>Mt-co3</i>, <i>Mt-nd1</i>, <i>Mt-nd2</i>, <i>Mt-nd4</i>, <i>Mt-nd5</i>, and <i>Mt-atp6</i>. Concurrently, stress response-related genes, such as <i>Selenop</i>, <i>GADD45B</i>, and <i>SIK2</i>, showed a down-regulation trend. These transcriptional changes are consistent with reduced expression of genes involved in antioxidant defense and cellular protection under high-flow conditions, integrating differential-expression and pathway-enrichment results. This decline correlates with the down-regulation of genes associated with antioxidant and stress regulation. Pathways related to energy metabolism show significant enrichment, suggesting enhanced regulation of energy supply and allocation. This pattern indicates metabolic reprogramming characteristics adapted to high-flow-velocity stress.