Integrated metabolomics and transcriptomics analyses characterize the tissue-specific flavonoid biosynthesis and quality formation in the ethnomedicine Melastoma dodecandrum

Melastoma dodecandrum Lour. is a prominent medicinal plant traditionally utilized in the southern China for treating gynecological inflammation disorders, representing significant potential for pharmaceutical development. However, systematic phytochemical characterization of this species remains incomplete, and the tissue-specific distribution and accumulation of its primary bio-activeflavonoids remain unclear. In this study, an integrated untargeted metabolomics and transcriptomic approach was employed to systematically elucidate the spatial distribution of flavonoids across the roots, stems, and leaves of M. dodecandrum, alongside the expression topology of key structural genes involved in their biosynthesis. Metabolomic profiling revealed that flavonoids -predominant flavonols- were significantly enriched in foliar and root tissues. A total of 20 major flavonoids were annotated, among which quercetin-3-O-glucosyl-(1→2)-rhamnoside emerged as the most abundant constituent in both leaves and roots, suggesting its pivotal role in the plant's pharmacological efficacy. Leveraging the published reference genome of M. dodecandrum for transcriptome analysis, we systematically identified key catalytic enzyme genes within the flavonoid biosynthetic pathway, including CHS, CHI, and DFR. Notably, their organ-specific expression patterns highly mirrored the accumulation dynamics of their corresponding metabolites. Furthermore, integrated KEGG pathway enrichment analysis demonstrated that flavonoid-specific metabolic pathways dictate the distinct chemophenotypic differentiation among different organs. In conclusion, this study decodes the molecular mechanism governing the chemical quality formation of M. dodecandrum, establishing a robust theoretical framework for the sustainable development and high-value utilization of this medicinalresource.