Objective This study aimed to screen key enzyme genes associated with the biosynthesis of gastrodin and parishin E in Gastrodia elata. Through comparative transcriptome sequencing following methyl jasmonate (MeJA) treatment. Methods Using both the corm (MTE and the symbiotic tuber (IMTC) as experimental materials, different concentrations (100—500 μmol/L) of MeJA were sprayed for varying durations (0—72 h). The content changes of gastrodin and parishins E were determined by HPLC. Transcriptomic and metabolomic analyses were performed on samples treated under the optimal MeJA conditions to mine key genes in the parishin E biosynthetic pathway. Results After 48 h of treatment with 300 μmol/L MeJA, the contents of all six target compounds were significantly increased. Specifically, the content of parishin E increased from 0.21 mg/g to 0.61 mg/g, representing an approximately 2.90-fold enhancement. Transcriptome sequencing generated 432.79 Gb of Clean Data and identified 18 886 expressed genes, including 2 389 novel genes. Differential expression analysis revealed 5 704 differentially expressed genes, with 2 635 up-regulated and 3 069 down-regulated. KEGG enrichment analysis showed significant enrichment in phenylpropanoid biosynthesis, plant signal transduction, and other secondary metabolism-related pathways. Through integrated analysis of expression patterns and compound accumulation trends, along with homology comparison, we identified two glycosyltransferase genes GeUGT, two citrate-CoA synthetase genes GeCCS, and two acyltransferase genes GeBAHD potentially involved in parishin E biosynthesis. Conclusion This study demonstrates that MeJA effectively regulates secondary metabolism in G. elata and identifies candidate genes (GeUGTs, GeCCSs, GeBAHDs) potentially associated with the biosynthesis of gastrodin and parishin E, providing a molecular foundation for elucidating the complete biosynthetic pathways of these key active compounds.

Gastrodia elata Bl.  /  parishin E  /  methyl jasmonate  /  gastrodin  /  omics analysis  /  biosynthesis