Integrated physiological and multi-omics analyses revealed the response mechanisms of Taxus yunnanensis to varying irrigation amounts

Taxus yunnanensis has attracted considerable attention due to its richness in bioactive metabolites, such as paclitaxel and flavonoids, and artificial cultivation has become its primary source. However, the mechanisms by which irrigation amount regulates plant growth, physiological traits, and secondary metabolism remain unclear. Therefore, five irrigation gradients (G1-G5) were established, and a systematic analysis was conducted by integrating growth, physiological, metabolomic, and transcriptomic data. The results demonstrated that decreasing irrigation levels significantly suppressed the growth of T. yunnanensis . Concurrently, the contents of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) increased progressively, indicating enhanced oxidative stress. The concentrations of osmolytes, including soluble sugars (SS), soluble proteins (SP), and proline (Pro), were significantly elevated, accompanied by a pronounced enhancement in antioxidant enzyme activities. Meanwhile, photosynthetic pigment contents declined substantially with reduced irrigation supply. Integrated metabolomic and transcriptomic analyses identified a total of 1526 differentially accumulated metabolites (DAMs) and 13,529 differentially expressed genes (DEGs). KEGG enrichment analysis revealed that DEGs and DAMs were primarily concentrated in pathways associated with flavonoid and paclitaxel biosynthesis. Further weighted gene co-expression network analysis (WGCNA) identified ten gene modules (ME1-ME10) that were significantly correlated with variations in irrigation levels. The ME1 and ME5 modules were positively correlated with flavonoid and paclitaxel levels, respectively. Both modules contained numerous candidate transcription factors (TFs) related to flavonoid and paclitaxel biosynthesis, including WRKY, LBD, MYB, bHLH, and HD-ZIP families. Overall, this study provides a scientific basis for optimizing irrigation management and regulating the accumulation of medicinally active constituents in T. yunnanensis . • Systematically analyzed the multi-omics characteristics of Taxus yunnanensis in response to different irrigation amounts. • Reduced irrigation inhibits growth and activates antioxidant and osmotic adjustment systems. • Irrigation alters flavonoid and paclitaxel accumulation patterns. • Identification of irrigation-related gene modules and transcription factors.