Transcriptomic analysis reveals differential gene expression and metabolic reprogramming in Coptis teeta Wall. under drought and heat stress

Introduction Abiotic stresses such as drought and heat severely impair plant growth, survival, and secondary-metabolite production, posing a major threat to moisture-dependent alpine medicinal plants. Coptis teeta Wall., a critically endangered species of the Eastern Himalayas valued for its isoquinoline alkaloids, is particularly vulnerable to climatic fluctuations. Methods In this study, RNA-Seq based transcriptome profiling was performed to decipher the molecular responses of C. teeta under drought and heat stress. Results Differential expression analysis identified 3,099 DEGs under drought, 816 under heat, and 3,790 under combined stress highlighting a strong and synergistic transcriptional reshaping under environmental extremes. Antioxidant enzymes including ascorbate peroxidase (APX), superoxide dismutase (SOD), and glutathione peroxidase (GPX) were significantly upregulated, whereas thioredoxin and glutaredoxin-associated redox regulators were suppressed, indicating a shift toward peroxidase-driven ROS detoxification. Major transcription factors (TFs) from the NAC, DREB, WRKY, bZIP, and HSF families exhibited strong stress-specific induction, with DREB2A, AREB1, and HSFA2 emerging as central regulatory hubs. Secondary-metabolite biosynthesis was distinctly modulated: early benzylisoquinoline alkaloid (BIA) pathway genes were upregulated, whereas downstream enzymes such as berberine bridge enzyme (BBE) and O-methyltransferases were downregulated, reflecting a stress-induced trade-off between alkaloid diversification and survival. GO and KEGG enrichment further revealed activation of protein folding, oxidoreductase activity, glutathione metabolism, and hormone-signaling pathways. Discussion Overall, this study provides the first genome-wide insight into transcriptional networks and metabolic reprogramming in C. teeta under abiotic stress, offering essential molecular resources for conservation, stress-tolerance enhancement, and genetic improvement.