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Updated: Jul 6, 2026
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Comparative Transcriptome and Metabolome Analyses Provide New Insights into the Molecular Mechanisms Underlying
Meiqiong Tang1, Chunying Liang2, Yude Peng1
1Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Engineering Research Center for Southwest Endangered Medicinal Materials Resources Development, National Center for TCM Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China.
Background:
F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound biosynthesis occurring during the root development of F. hirta are unknown.
Method:
Transcriptome and widely targeted metabolome analyses were performed to investigate gene expression and metabolite variation during the development of F. hirta taproots.
Results:
A total of 3792 differentially expressed genes (DEGs) were identified between the one- and three-year-old F. hirta taproots; they are related to circadian rhythm-plant, phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant-pathogen interaction pathways. In total, 119 differentially accumulated metabolites (DAMs) were identified between the one- and three-year-old F. hirta taproots, including flavonols, phenolic acids, and coumarins compounds. Integrative transcriptome and metabolome analyses revealed a significant correlation between 172 DEGs and 21 DAMs; they were predominantly enriched for processes associated with phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and stilbenoid, diarylheptanoid, and ginerol biosynthesis. In addition, 26 DEGs were identified to be significantly correlated with the DAMs that accumulated in the phenylpropanoid biosynthesis pathway, and these DEGs may be the key genes for the biosynthesis of F. hirta active compounds.
Conclusions:
The phenylpropanoid biosynthesis pathway plays a dual role in both development and bioactive compound synthesis in F. hirta taproots. These findings provide a molecular regulatory network in the relationships between F. hirta taproot development and the accumulation of secondary metabolites. The identification of candidate genes and pathways provides a genetic resource for quality control and future molecular breeding in F. hirta.
