Identification and characterization of tissue-specific genes in response to handling stress in topmouth culter ( <i>Culter alburnus</i> ) kidney, liver and muscle tissues

Topmouth culter ( Culter alburnus ) is China’s important freshwater economic fish. However, external stressors frequently provoke intense responses, leading to low survival rates and diminished productivity. The absence of stress-related genes has significantly limited our understanding of stress response in this fish. Therefore, 85,846,206 high-quality reads were acquired from kidney, liver, and muscle cDNA libraries of topmouth culter using Illumina sequencing technology in this study. Comparative analysis revealed that 3,158, 409, and 1,952 unigenes were specifically expressed in the kidney, liver, and muscle transcriptome. Additionally, 83 crucial tissue-specific genes were identified within three stress-related GO terms: response to stimulus (GO:0050896), response to stress (GO:0006950) and response to hypoxia (GO:0001666). From these, 18 tissue-specific genes were further isolated. During the short-term stress experiment (two repeated handling stress, including chasing 2 min and netting out of water for 30 sec), significant changes were observed in the cortisol levels of both the treatment and recovery groups. Furthermore, notable changes were noted in the expression of LCP2 , PTK2b, and P-selectin genes in the kidney; FABP1 , IGFBP1, and CYP4V2 genes in the liver; and MYH10 , Myogenin 2 and Troponin C genes in the muscle of topmouth culter in the treatment and recovery groups ( P &lt; 0.05). The tissue-specific transcriptome profiles generated in this study offer valuable insights into the molecular and functional mechanisms associated with stress response in topmouth culter. We characterized genes related to stress response in tissues such as the kidney, liver, and muscle; these findings offer novel insights into stress research in fish. We can further explore the breeding of strains with enhanced stress resistance and promote the healthy development of topmouth culter industry.