A telomere-to-telomere reference genome for Rosa roxburghii reveals lineage-specific diversification of triterpenoid biosynthesis

Abstract Rosa roxburghii ( RRT ) is a nutritionally and medicinally important Rosaceae species that accumulates diverse bioactive compounds, making it an excellent system for investigating the genetic basis and evolutionary diversification of specialized metabolism. Here, we report a complete telomere-to-telomere (T2T), gap-free genome assembly of the elite cultivar ‘Guinong No. 5’ ( RRT5 ), comprising 494.57 Mb with a contig N50 of 51.44 Mb and a base accuracy of over 99.99%. Of this assembly, 99.9% were anchored to seven pseudo-chromosomes. Multi-omics analyses identified OSC , CYP , and UGT genes potentially involved in triterpenoid biosynthesis, while gene–metabolite correlation analyses highlighted MYB30 and MYB31 as candidate regulators of multiple triterpenoids. Notably, the biosynthetic capacities for Kaji-ichigoside F1 and rosamultin vary across lineages within Rosoideae, likely reflecting lineage-specific gene gain or loss and/or evolutionary divergence in regulatory pathways. Together, the RRT5 genome, transcriptome, and profiling of the eight key triterpenoids provide a valuable resource for elucidating triterpenoid biosynthesis, regulation, and evolution, and for guiding genome-informed breeding of R. roxburghii .