Integrative metabolomic and transcriptomic analyses reveal flavonoid biosynthesis pathway in Eupatorium lindleyanum

Eupatorium lindleyanum, a medicinal plant from the Asteraceae family, is renowned for its diverse bioactive compounds, particularly flavonoids, which contribute to its various pharmacological activities. However, the biosynthetic pathway and regulatory mechanisms underlying flavonoid production in Eupatorium lindleyanum remain largely unexplored. In this study, an integrated metabolomic and transcriptomic approach was employed to investigate flavonoid biosynthesis in Eupatorium lindleyanum. Samples from four different tissues (roots, stems, leaves, and flowers) were analysed to identify variations in differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). A total of 330 differentially accumulated flavonoid metabolites (DFMs) and 53,610 DEGs were identified. A total of 27 key structural genes involved in the flavonoid synthesis pathway, including PAL, 4CL, C3H, F3H, FLS, and ANS, and others were found to be significantly activated in specific tissues. Additionally, 69 transcription factors (TFs) from five families, including AP2/ERF, NAC, WRKY, MYB, and bHLH, were identified as potentially involved in regulating flavonoid biosynthesis. The findings of this study offer crucial information on the genes and metabolites involved in flavonoid metabolism in Eupatorium lindleyanum. The identification of key genes and TFs, along with an understanding of their regulatory networks, can facilitate the development of new cultivars with increased flavonoid contents and improved medicinal value.