Comparative plastid genome analyses of Rosa: Insights into the phylogeny and gene divergence

The genus Rosa comprises more than 150 species spread across three subgenera, Hesperhodos, Hulthemia, and Rosa, most of which have high economic and ecological values. Here, we report 31 complete plastomes that belong to the genus Rosa, with the aim of better understanding the evolution and divergence of genes of the plastome in this genus. A comparative analysis was conducted to characterize the chloroplast genomes of 12 taxa that cover all the sections in the three subgenera of Rosa. Further, complete chloroplast genome sequences revealed six hotspots of nucleotide polymorphism, including five intergenic regions and one coding sequence. In addition, a pairwise analysis revealed that R. stellata and R. berberifolia have the highest average genetic distances (Da) and nucleotide divergence (Dxy) compared with other species. Moreover, the lowest Da and Dxy was observed between R. gallica and R. canina, followed by R. multiflora and R. chinensis var. spontanea. The phylogenetic relationships within Rosa inferred from the 44 chloroplast genomes revealed the R. subg. Hesperhodos is the clade that diverged the earliest. Its successive clades were identified as R. subg. Huithemia and R. sect. Pimpinellifolia. The phylogenomic analysis also revealed rapid simultaneous diversification within the Rosa subgenus. Significant increases in Pi and dN for ycf1, dN/dS for ycf2 were observed across the genus. Finally, we found that most RNA editing sites identified in the genus are section-specific, suggesting that the subgenera or sections have a self-evolving lineage. Taken together, the plastome information is valuable for species identification, phylogenetic studies, molecular genetics and breeding Rosa species.