Molecular characterization and gene expression of the HSP90 gene family in Cyprinus carpio and Oreochromis niloticus under thermal stress.

Heat Shock Proteins (HSPs) act as molecular chaperones, protecting cells by stabilizing and refolding damaged proteins under stress. While the induction of HSPs in fish under stress is well-documented, comprehensive genome-wide analyses of the entire HSP90 gene family in a comparative context remains limited. This study provides a systematic, comparative analysis of the HSP90 gene family in two economically important species with distinct thermal niches, Cyprinus carpio (common carp) and Oreochromis niloticus (Nile tilapia). Our investigation included phylogenetic relationships, motif patterns, physicochemical properties, positive selection, and expression profiles. Key findings include the identification of tandem duplications in both species and a higher number of transcription factor-binding sites (TFBSs) in tilapia compared to common carp. Positive selection analysis revealed significant evidence of adaptive evolution in the HSP90 proteins. qRT-PCR analysis revealed organ-specific responses and differing thermal tolerances, with O. niloticus exhibiting a more pronounced adaptive response to extreme heat (40 °C). These findings provide valuable insights into the evolutionary dynamics and functional divergence of the HSP90 gene family, offering a theoretical basis for understanding genetic adaptations to thermal stress. As global temperatures rise, such insights are essential for enhancing aquaculture sustainability by leveraging natural adaptive mechanisms.