Genome-wide identification and stress-responsive expression of Panax notoginseng Hsp gene superfamily

Panax notoginseng cultivation is threatened by climate change-induced multistress, leading to substantial yield losses and jeopardizing supply of its bioactive compounds. Heat shock proteins (Hsps) are molecular chaperones crucial for maintaining proteostasis under multistress, yet their systematic characterization in P. notoginseng limiting our understanding of their potential utility in molecular breeding programs for this specialty plant. Here, we performed the first genome-wide analysis of the Hsp superfamily in P. notoginseng, identifying 68 PnHsp genes classified into six subfamilies. Phylogenetic analysis revealed evolutionary conservation of Hsp60/70/90/100 orthologs with Arabidopsis, while Hsp20 members exhibited species-specific divergence. Promoter analysis identified 2505 stress- and hormone-responsive cis-regulatory elements. Collinearity analysis indicated that segmental duplication events, all under purifying selection, contributed to the expansion of this gene family. Critically, integrated transcriptome and WGCNA analyses revealed PnHsp20–1 and PnHsp20–10 as important nodes in a protein quality control network activated by diverse stresses. This role is structurally substantiated by a high-confidence model showing PnHsp20–10 binding to the DXPS enzyme, providing mechanistic insight into its chaperone function during multistress adaptation. These findings provide a valuable genomic resource and candidate gene pool for future development of Hsp-targeted breeding strategies aimed at enhancing multistress resilience in P. notoginseng, which is essential for safeguarding the sustainable production of this high-value medicinal plant.