Panax quinquefolius 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-O-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 PqUGT71A1 catalyzes apigenin and naringenin glycosylation at the 7-OH position. Additionally, subcellular localization and yeast one-hybrid assays demonstrated that PqMYB7 and PqMYB13 interact with the PqUGT71A1 promoter and activate its expression.. This study unveils the spatial dynamics of flavonoid metabolism in P. quinquefolius and establishes a MYB-UGT regulatory axis, providing critical insights for metabolic engineering and bioactive compound optimization in medicinal plants.

Perilla frutescens (L.) Britt. is a traditional medicinal and culinary plant with a long history of cultivation and significant potential for broader utilization. The basic helix-loop-helix (bHLH) gene family is essential for regulating plant growth, development, stress responses, and secondary metabolism. However, the bHLH gene family in P. frutescens has not yet been characterized. In this study, a total of 205 bHLH genes were identified in P. frutescens through genome mining and analysis. Phylogenetic analysis classified these PfbHLH genes into 23 distinct subfamilies. Promoter analysis revealed an enrichment of cis-acting elements linked to plant hormone signaling and stress responses, suggesting their potential regulatory roles in development, growth, and stress adaptation. Expression profiling based on publicly available RNA-seq data demonstrated tissue-specific expression patterns of PfbHLH genes in roots, stems, and leaves. Four PfbHLH genes (PfbHLH66, PfbHLH45, PfbHLH13, and PfbHLH5) showed significant responses to methyl jasmonate (MeJA) induction. Yeast one-hybrid assays confirmed that these PfbHLH proteins could bind to the cis-acting G-box (CACGTG) element. This study offers new perspectives on the evolution, regulatory mechanisms, and functional roles of the bHLH gene family in P. frutescens. The findings deepen our understanding of the functional diversity within this gene family and establish a foundation for genetic enhancement and the biosynthesis of medicinal compounds in the species.