A <i>Rosa</i> pangenome to advance rose genomics, phylogenetics and breeding

Abstract Rosa, belonging to the family Rosaceae, encompasses more than 150 species widely distributed across the northern hemisphere. Renowned for their beauty, roses are cultivated throughout the world for ornamental purposes and the production of essential oils and perfumes. Despite their cultural and commercial significance, the genomic resources of wild Rosa species have not been studied comprehensively, hampering the understanding of their genetic diversity, evolutionary history, and breeding potential. Here we present a Rosaceae panproteome and a Rosa pangenome, spanning wild, traditional garden, and modern rose lineages, constructed using a De Bruijn graph (DBG)-based approach, and introduce two high-quality de novo genomes for Rosa sericea and Rosa rugosa. A phylogeny of 18 Rosa haplotypes based on 4367 single-copy core homology groups (genes) provided robust evolutionary inference. Our analysis revealed substantial interspecific genomic diversity in core gene repertoires, structural features, and a transposable element (TE) landscape that shaped genome size differences and is potentially linked to phenotypic plasticity. We provide two examples of the types of analyses that become possible with this pangenome. First, the pangenome serves as a quality-aware lens, exposing discrepancies arising from assembly and annotation variability and helping separate technical artifacts from genuine biological signal. Second, the pangenome provides locus-level resolution: analysis of MYB114, a key regulator of anthocyanin accumulation, reveals lineage-specific presence–absence patterns and TE-associated regulatory variation. This pangenomic study deepens our understanding of the genetic diversity and genome evolution of Rosa species and establishes a resource to resolve the genetic bases of key traits, thereby informing and supporting rose breeding.