Integrated Transcriptomic and Metabolomic Analysis Reveals Tissue-Specific Flavonoid Biosynthesis and MYB-Mediated Regulation of UGT71A1 in Panax quinquefolius

<i>Panax quinquefolius</i> is a globally valued medicinal plant rich in bioactive flavonoids, yet the molecular mechanisms underlying their biosynthesis remain poorly understood. In this study, we integrated transcriptomic and metabolomic analyses to investigate tissue-specific flavonoid accumulation and regulatory networks in roots, leaves, and flowers. Metabolomic profiling identified 141 flavonoid metabolites, with flavones, flavonols, and C-glycosylflavones predominantly enriched in aerial tissues (leaves and flowers), while specific glycosides like tricin 7-<i>O</i>-acetylglucoside showed root-specific accumulation. Transcriptome sequencing revealed 15,551-18,946 DEGs across tissues, and the reliability of the transcriptomic data was validated by qRT-PCR. KEGG and GO annotation analyses suggested that these DEGs may play a crucial role in the biosynthesis and metabolism of secondary metabolites. From the DEGs, UGTs and MYB TFs were identified and subjected to correlation analysis. Functional validation through in vitro enzymatic assays confirmed that <i>PqUGT71A1</i> catalyzes apigenin and naringenin glycosylation at the 7-OH position. Additionally, subcellular localization and yeast one-hybrid assays demonstrated that <i>PqMYB7</i> and <i>PqMYB13</i> interact with the <i>PqUGT71A1</i> promoter and activate its expression.. This study unveils the spatial dynamics of flavonoid metabolism in <i>P. quinquefolius</i> and establishes a MYB-UGT regulatory axis, providing critical insights for metabolic engineering and bioactive compound optimization in medicinal plants.