Integrative genomic, transcriptomic, and metabolomic profiling of Dillenia suffruticosa

The genus Dillenia, a basal core eudicot native to Southeast Asia and the Indian Ocean islands, is prized for its wide-ranging medicinal and ornamental applications. This study generated and integrated a chromosome-scale reference genome for D. suffruticosa spanning 599 Mb with 26 chromosomes (N50:24.1 Mb) encoding 28,248 genes using organ-resolved transcriptomics and untargeted metabolomic analysis. The root metabolome is dominated by triterpenoids, including lupeol, α-/β-amyrin, and betulinic acid, whose abundance mirrors a selective cytotoxic profile against a panel of 10 cancer cell lines. Ethanol extracts were active against 7 of 10 lines (IC₅₀ = 92-194 µg mL⁻¹), while SFE extracts were active against 6 lines (IC₅₀ = 91-234 µg mL⁻¹), with limited or no activity observed in the remaining lines (IC₅₀ > 300 µg mL⁻¹). Although the specific bioactive compound(s) remain unresolved, genome annotation identified candidate oxidosqualene cyclases and downstream putative cytochrome P450 monooxygenases and UDP-glycosyltransferases, indicating the presence of genes associated with triterpenoid biosynthesis. Together, these chemogenomic resources illuminate the molecular basis of specialized metabolism in D. suffruticosa and establish a platform for future studies on its ecological functions and the discovery of plant-derived therapeutic candidates.