Integrated Transcriptomic and Metabolomic Analyses Uncover the Molecular Mechanisms Underlying Drought Tolerance in Isodon suzhouensis

Background/Objectives: This study aims to reveal the physiological and molecular regulatory mechanisms of the genuine medicinal herb I. suzhouensis K. F. Zhai, Z. B. Han & S. B. Zhou (Wangzaozi) of Anhui province in response to drought stress, and clarify the regulatory patterns of drought adversity on the accumulation of its medicinal active ingredients. Methods: Mild natural drought treatment was applied to I. suzhouensis. Combined with Illumina high-throughput transcriptome sequencing and HPLC-MS/MS targeted metabolomics detection, this study jointly deciphered the dynamic changes in gene expression and metabolite accumulation of I. suzhouensis under drought. Key drought-responsive metabolic pathways, core regulatory genes and marker metabolites were screened. Results: A total of 56,823 high-quality unigenes were obtained via transcriptome sequencing, among which 23,580 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that DEGs were predominantly enriched in pathways, including plant hormone signal transduction, phenylpropanoid biosynthesis, flavonoid biosynthesis and photosynthesis. A total of 4171 metabolites were qualitatively and quantitatively characterized via metabolomics, and 1632 differentially expressed metabolites (DEMs) were screened, mainly enriched in phenylpropanoid biosynthesis, tyrosine metabolism, flavone and flavonol biosynthesis pathways. Physiological measurements of antioxidant indices demonstrated that the activities of SOD and POD increased by approximately 2-fold, while PAL activity rose by 1.55-fold, and chlorophyll content decreased significantly. Multi-omics joint analysis indicated that mild drought stress modulates the expression of genes involved in phenylpropanoid, flavonoid and diterpenoid biosynthetic pathways, alters antioxidant enzyme activities, and coordinately regulates the formation of drought tolerance and the accumulation of bioactive compounds in I. suzhouensis. Conclusions: This study systematically elucidates the drought response mechanism of I. suzhouensis cultivated in northern Anhui province. It provides theoretical evidence and candidate core responsive gene resources for standardized cultivation of I. suzhouensis and precise regulation of medicinal quality in drought-prone production areas.