Integrated Analysis of Transcriptome and Metabolome in Cirsium japonicum Fisch ex DC

[Image: see text] Cirsium japonicum Fisch ex DC belongs to the Compositae family and has been used as a folk remedy source in Asian countries because of its health-promoting properties. It is known that C. japonicum contains flavonoids, furans, long-chain alcohols, sterols, and volatile oils. Nevertheless, the molecular mechanism of secondary metabolite biosynthesis remains poorly understood. Therefore, transcriptome analysis and metabolic profiling were performed using different parts of C. japonicum to investigate phenylpropanoid metabolism. Based on the BLASTX search results, we identified 29 orthologs of enzymes responsible for phenylpropanoid biosynthesis. Additionally, 75 metabolites were identified in C. japonicum. Most of the flavonoid biosynthetic genes were significantly expressed ranging from 2.6- to 500-fold higher in the flowers than those in the leaves. Correspondently, the total content of flavonols was 21-fold higher in the flowers than in the roots. However, the total level of flavones showed 58-fold higher amounts in the leaves than in the flowers. Additionally, the total content of flavanols was 19-fold higher in the leaves than in the roots. The results of this study provide transcriptomic and metabolic information to elucidate the tissue-specific phenylpropanoid metabolism of C. japonicum.