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BackgroundSpecies of the genus Rosa are among the commercially important exploited groups of ornamental plants in the world. Despite its wide application, the phylogenetic placement of many subgenera and sections of the genus is still unresolved due to hybridization, polyploidization, incomplete lineage sorting, low differentiation among the genus, and even their complex history of cultivation and breeding. Through more comprehensive taxon sampling, this study analyzed 18 representative Rosa plastid genomes, including 13 new sequences, to elucidate their phylogeny within the genus as well as the variation patterns in the plastid genomes.ResultsThe results revealed that the length of 106 complete Rosa plastomes varied between 156,333 bp and 157,396 bp, with closed circular tetrad structures of the SSC and LSC regions separated by two IR regions. Comparative analysis subsequently revealed high similarity in the total GC content, gene order and PCGs (79) of Rosa plastomes. No significant contraction or expansion of the IR boundary was noted in most Rosa species, except for the trnH-GUG gene, which is found mainly in the LSC region but crosses the IRa/LSC boundary in basal taxa of the Rosa phylogenetic tree. Abundant SSRs (73-87) and long repeat sequences (36-52) were detected in Rosa plastomes, and most of these repeats could be found within the IGS region. Eight IGS regions were identified as highly variable regions, which provides potential information for developing molecular markers. Nineteen genes were discovered to have undergone significant positive selection. Phylogenetic analyses based on PCGs and complete plastome sequences indicated that the genus Rosa was monophyletic well grouped into seven major clades with high bootstrap support. Most previously-defined subgenera and sections were paraphyletic.ConclusionsBy assembling the largest known dataset of Rosa plastomes, the plastid genomic features across the genus were comprehensively studied before reconstructing a phylogenetic tree with a well-resolved backbone. However, the current study also shows the limitations of using plastomes to infer the phylogeny of some difficult taxa, and combining plastome, morphological and nuclear data together is recommended. This work offers valuable and basic sequence information for phylogenetic studies, species identification, Rosa species breeding and molecular genetics studies.