Semah mahseer (Tor douronensis) is a high-value freshwater cyprinid native to Southeast Asia. This study characterized acute transcriptomic responses in liver and white skeletal muscle following 6 h exposure to hyperthermia (35 °C), hypoxia (dissolved oxygen 2 mg/L), or their combination. Thirty-two RNA-seq libraries yielded approximately 48,504 annotated unigenes. Relative to the control, hyperthermia produced 7776 differentially expressed genes (DEGs) in liver and 1121 in muscle, hypoxia produced 2451 and 318 DEGs, and combined exposure produced 4952 and 717 DEGs, respectively. The response involved heat-shock proteins, endoplasmic-reticulum protein processing, glycolytic and oxygen-sensing pathways, mitochondrial and contractile programs, and apoptosis-associated signaling. Expression directions for 20 selected transcripts were compared by qRT-PCR; the reported cross-platform correlation was r = 0.91, although interpretation remains conditional on validation of reference-gene stability. Qualitative scanning electron microscopy showed region-dependent disruption of skeletal-muscle organization under the stress treatments. Because the study used one acute endpoint, two replicate tanks per condition, a de novo transcriptome, and no direct postmortem flesh-quality measurements, the findings should be interpreted as mechanistic hypotheses requiring independent validation.

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