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. 2024 Jun 22;15(7):828.
doi: 10.3390/genes15070828.

Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl

Xinchun Mo  1 , Ling Wang  1 , Chenghua Yu  1 , Can Kou  1
Affiliations

Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl

Xinchun Mo et al. Genes (Basel). .

Abstract

Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of Polygonatum kingianum Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in P. kingianum Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (HCT, CCOMT, C4H, C3'H, CHI, PGT1, FLS, F3'H, CHS, ANR, DFR, F3'5'H, and LAR) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in P. kingianum Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species.

Keywords: Polygonatum kingianum Coll.et Hemsl.; combined metabolomics and transcriptomics analysis; flavonoid biosynthesis; medicinal plant; roots.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Multivariate statistical analysis in the WR and RR of P. kingianum Coll.et Hemsl. (A). PCA analysis on WR and RR group. (B). Cluster heatmap of the WR and RR samples and metabolite classification. The cluster lines on the left represent the metabolite clusters. The cluster lines at the top represent sample clusters. Red and green indicate high and low metabolite contents, respectively. (C). PLS-DA score plots of WR and RR. (D). Volcano plot of differential metabolites. Red plot represent up-regulate, green plot mean down-regulate whereas gray represent not significant.
Figure 2
Figure 2
KEGG pathway enrichment of the differential metabolites in WR and RR of P. kingianum Coll.et Hemsl. (A) KEGG differential metabolite classification diagram. The ordinate is the name of the KEGG metabolic pathway, and the abscissa is the number of metabolites indicated by this pathway and its percentage associated with the total number of metabolites annotated. (B) Scatter diagram of the enrichment of differential metabolites in KEGG pathways.
Figure 3
Figure 3
Heat maps of flavonoid metabolites biosynthesis in WR and RR of P. kingianum Coll.et Hemsl.
Figure 4
Figure 4
Volcano map of DEGs identified from WR and RR of P. kingianum Coll.et Hemsl. The abscissa is the variation in gene expression (log2FC), and the ordinate is the significant level of differentially expressed genes (-log10FDR). The green dots represent the DEGs was down-regulated, and the red dots represent the DEGs was up-regulated, and the gray dots meant the DEGs was insignificantly regulated.
Figure 5
Figure 5
(A) GO and KEGG annotation of DEGs identified from WR and RR of P. kingianum Coll.et Hemsl. GO annotation of DEGs in WR and RR. (B) KEGG annotation of DEGs in WR and RR.
Figure 6
Figure 6
Top 20 transcript factor families (TFs) identified from WR and RR of P. kingianum Coll.et Hemsl. The transcription factor families involved in regulation of the biosynthesis of flavonoids was labeled with green color.
Figure 7
Figure 7
Correlation analysis between transcriptome and metabolome in WR vs. RR. (A) The genes correlation and components between WR and RR are shown by the nine-quadrant diagram. The abscissa represents the log2FC of the genes, and the ordinate represents the log2FC of the metabolites. (B) KEGG enrichment analysis of DEGs (blue column) and DAMs (red column) enriched in the same pathway. The red color represent the metabolites and the blue color represent the genes.
Figure 8
Figure 8
Correlation network analysis of flavonoid derivatives biosynthesis in WR and RR of P. kingianum Coll.et Hemsl. (A) Correlation network of DEGs and DAMs in flavonoid biosynthesis pathway. (B) Correlation network of DEGs and DAMs in isoflavonoid biosynthesis. (C) Correlation network of DEGs and DAMs in flavone and flavonol biosynthesis. Green and red ovals represent metabolites and genes, respectively. Solid line represents positive correlation, and dash line represents negative correlation.
Figure 9
Figure 9
Validation of 10 DEGs by qRT-PCR in WR and RR. The X-axis mean genes in WR and RR. The left Y-axis represents the relative expression of each gene in WR and RR by qRT-PCR.
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