Genome-wide identification of heat shock protein gene family and their response to chronic heat stress in skeletal muscle of black rockfish (Sebastes schlegelii)

Functioning as molecular chaperones, heat shock proteins (HSPs) are rapidly upregulated under stress conditions, safeguarding cells against damage induced by heat, mechanical injury, and chemical agents. Despite their critical physiological roles, a comprehensive genome-wide characterization of HSP genes has been lacking for Sebastes schlegelii, a commercially important coastal benthic fish. In this study, we systematically identified the HSP gene family and analyzed its expression profiles. A total of 103 HSP genes were identified within the S. schlegelii genome. Phylogenetic analysis (interspecific and intraspecific analyses), coupled with conserved motif and domain characterization, classified these HSPs into six subfamilies: Hsp20 (Hspb), Hsp40 (Dnaja/Dnajb/Dnajc), Hsp60 (Hspd1/Cct/Bbs), Hsp70 (Hspa), Hsp90, and Hsp100 (Clp). Motif and domain analyses revealed significantly higher sequence conservation within the Hsp70 and Hsp90 subfamilies compared to other HSP groups. Chromosomal mapping indicated that HSP genes are distributed across all 24 chromosomes of S. schlegelii, albeit with varying densities. Gene duplication analysis identified 6 whole-genome/segmental duplication events and 3 tandem duplication pairs within the HSP family. The observed Ka/Ks ratios (<1) provide evidence for purifying selection acting on these sequences. Protein-protein interaction (PPI) network analysis predicted that Hsp70 subfamily members potentially receive regulatory inputs from other subfamilies, while Hsp40 members primarily functioned as co-chaperones. Notably, Hsp genes are ubiquitously expressed across the ten adult tissues, with the majority of family members (70.87 %) exhibiting the highest expression in the brain and ovarian tissues, suggesting coordinated functions in fundamental cellular processes. Following one month of chronic heat exposure (27 °C), S. schlegelii significantly upregulated 16 chaperone genes, indicating transcriptome-level thermal adaptation. This study provides the first systematic characterization of the HSP gene family in S. schlegelii, establishing a foundation for future functional investigations and identifying potential genetic targets for breeding thermotolerant aquaculture strains.