Comparative Analysis of the Complete Chloroplast Genome of Mainland and Other Species.

, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland and compared it with those of the island type and other species. The chloroplast genome of mainland is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two lines and the other species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All species clustered into a monophyletic group, but the chloroplast genome of mainland was more similar to the other species than to that of the island . The and genes were detected to be under positive selection within the lineage compared to other related taxa. The complete chloroplast genome of mainland presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the genus and the Asteraceae.