The Rosa roxburghii genome provides insights into triterpenoid metabolism

Rosa roxburghii is a horticultural crop valued for its nutritional and medicinal properties, which is largely attributed to the diverse bioactive triterpenoids in its fruits. In this study, we provided a multi-omics insight into the triterpenoid biosynthesis in R. roxburghii. We first generated a high-quality chromosome-scale genome assembly of the cultivated variety "Guinong No.5", with a final genome size of 512.5 Mb. Subsequent genomic analyses indicated the absence of recent whole-genome duplication events, and pointed triterpenoid metabolism as a primary pathway undergoing pronounced genomic innovation. Genome-wide identification of triterpenoid biosynthesis-related families revealed 22 squalene epoxidase (SQLE) and 14 oxidosqualene cyclase (OSC) genes. Both families possessed weak codon usage bias, yet they exhibited distinct evolutionary paths. The upstream SQLEs have undergone significant expansion, primarily via tandem duplications, whereas the downstream OSCs family remained constrained and experienced gene loss. Integrated transcriptomic and metabolomic profiling across fruit developmental stages demonstrated that the upregulation of specific RroSQLEs (e.g. RroSQLE15 and RroSQLE16) correlated with the total triterpenoid accumulation, while the downregulation of specific RroOSCs (e.g. RroOSC4 and RroOSC13) was associated with a shift in triterpenoid composition, particularly a reduction in triterpenoid saponin abundance. Collectively, our findings suggest a decoupled evolutionary strategy between upstream precursor supply and downstream diversification in triterpenoid biosynthesis in R. roxburghii, providing a valuable genomic resource and a prioritized set of candidate genes for future metabolic engineering and quality improvement of this functional fruit crop.