Evolutionary and phylogenetic analyses of 11 species based on the complete chloroplast genome.

The subgenus , one of the most important groups in the genus , comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known species. Here, we report the chloroplast (cp) genome sequences of 11 species to provide insight into evolution of the plastome. The cp genomes of the 11 species (157,571-158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including , , , -, -, and -. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the , , , and genes; whereas , , , , and showed a signature of possible positive selection during the course of evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which was separated as an independent subclade. was genetically closer to , , and () than to members of true cherry, whereas and were most closely related to and . However, formed a clade with , , × 'Gisela 6', and as a true cherry group. These results provide new insights into the plastome evolution of , along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of species.