Transcriptome and Metabolome Analysis Reveal the Reasons for the Formation of Tissue Specificity and Quality in the Underground Part of <i>Saposhnikovia divaricata</i> (Turcz.) Schischk

Saposhnikovia divaricata, obtained from the desiccated roots of the plant Saposhnikovia divaricata (Turcz.) Schischk, is a medicinal material with its phloem known to be richer in chromones than its xylem. To understand this disparity, we compared the xylem and phloem using high-performance liquid chromatography (HPLC), transcriptomics, and nontargeted metabolomics. HPLC revealed that cimifugin was six times higher in the phloem. Conversely, prim-O-glucosylcimifugin and 4'-O-β-D-glucosyl-5-O-methylvisamminol were 1.2 and 1.6 times more abundant in the xylem, respectively (p < 0.01). Transcriptome sequencing identified nine differentially expressed genes, predominantly involved in phenylpropanoid biosynthesis (PAL, HCT, CCR, CSE, COMT, and CCoAOMT). Nontargeted metabolomics identified 229 differential metabolites, also largely enriched in phenylpropanoid biosynthesis. Integrated analysis revealed a strong positive correlation between the gene COMT and two metabolites (trans-cinnamaldehyde and myricatomentoside I), identifying COMT as a key candidate gene governing quality. Our findings demonstrate that phenylpropanoid, flavonoid, and lignin biosynthesis pathways crucially impact secondary metabolite accumulation in Saposhnikovia divaricata, providing new insights for its exploitation.