Integrated Transcriptomic and Metabolomic Analysis Reveals MeJA-Mediated Flavonoid Biosynthesis in Cyclocarya paliurus Callus

Cyclocarya paliurus is a rare Chinese endemic medicinal tree with high-value bioactive metabolites in its leaves, but wild resource scarcity and growth constraints limit large-scale utilization. Callus culture combined with methyl jasmonate (MeJA) elicitation is a promising strategy for sustainable bioactive compound production. However, the metabolic responses of C. paliurus callus to MeJA and the underlying molecular regulatory mechanisms remain unclear. Here, in vitro C. paliurus callus treated with gradient concentrations of MeJA was analyzed by integrating untargeted metabolomics and transcriptomics. Exogenous MeJA significantly induced the accumulation of major flavonoids in C. paliurus callus, including dihydrokaempferol, dihydroquercetin, and quercetin. Twelve key structural genes involved in flavonoid biosynthesis (two 4CL genes, two CHS genes, one CYP73A gene, three HCT genes, one CCoAOMT gene, one CHR gene, one CYP75A gene, and one ANS gene) were co-upregulated. Two hub transcription factors (TFs), CpbHLH162 and CpNAC073, were identified as potential upstream regulators of flavonoid synthesis. These findings indicate that MeJA enhances flavonoid production in C. paliurus callus by activating multiple structural genes and key transcription factors, providing candidate genes for metabolic improvement and theoretical support for the large-scale industrial production of bioactive compounds in C. paliurus.