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. 2025 Mar 16;26(6):2669.
doi: 10.3390/ijms26062669.

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

Yumeng Wang  1 , Jiaxin Zhang  1 , Ping Wang  1 , Yongkang Li  2 , Yihan Wang  1 , Yan Yan  1 , Junwen Chi  1 , Jiankang Chen  1 , Junmei Lian  1 , Xiangmin Piao  1 , Xiujuan Lei  1 , Ying Xiao  2 , Jeremy Murray  3 , Micheal K Deyholos  4 , Yingping Wang  1 , Peng Di  1 , Jian Zhang  4   5
Affiliations

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

Yumeng Wang et al. Int J Mol Sci. .

Abstract

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.

Keywords: American ginseng; Panax quinquefolius; flavonoid biosynthesis; transcriptomic and metabolomic integration study.

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Conflict of interest statement

This research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Analysis of Metabolite Accumulation Characteristics Across Three Tissues of P. quinquefolius (A) PCA of flavonoid metabolites in different tissues of P. quinquefolius. (B) Bar chart displaying the number of differentially accumulated metabolites among the tissues. (C) Clustering heatmap of flavonoid metabolites in different tissues of P. quinquefolius. Red indicates high abundance of metabolites, while blue represents relatively low abundance.
Figure 2
Figure 2
Analysis of DEGs Among Three Tissues of P. quinquefolius (A) Volcano plots of DEGs in comparisons between Flower_vs._Root, Flower_vs._Leaf, and Leaf_vs._Root. (B) GO annotation of DEGs. (C) KEGG enrichment analysis of DEGs.
Figure 3
Figure 3
qRT-PCR Validation of DEGs randomly selected from three tissues of P. quinquefolius.
Figure 4
Figure 4
Integrated metabolomic and transcriptomic analysis across three tissues of P. quinquefolius, (A) Nine-quadrant plot of genes and metabolites. (B) Correlation analysis of DEGs and DAMs selected from the third and seventh quadrants.
Figure 5
Figure 5
Flavonoid biosynthesis pathway in P. quinquefolius. Square heatmaps represent the expression levels of differentially expressed key enzyme genes across different tissues, while circular heatmaps represent the accumulation levels of differentially accumulated flavonoid metabolites in various tissues.
Figure 6
Figure 6
Functional validation of PqUGTs and PqMYBs in P. quinquefolius. (A) Correlation analysis of 27 highly expressed PqUGTs and 13 PqMYBs. (B) Phylogenetic analysis of the amino acid sequences of selected PqUGTs and UGT genes from various plant species, with the selected candidate genes highlighted in the blue box. (C) UPLC-MS chromatogram showing the catalytic product of PqUGT19 with apigenin as the substrate. (D) UPLC-MS chromatogram showing the catalytic product of PqUGT19 with naringenin as the substrate. (E) Subcellular localization of PqMYB7, PqMYB9, and PqMYB13 in vivo. (F) Yeast one-hybrid assay demonstrating the interaction of PqMYB7 and PqMYB13 with the PqUGT19 promoter.
Figure 7
Figure 7
Schematic representation of the MYB-UGT regulatory axis in flavonoid biosynthesis in P. quinquefolius.
See this image and copyright information in PMC

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