Comparative And Phylogenetic Analysis Of The Complete Chloroplast Genomes Of Threepaeoniasectionmoutanspecies (Paeoniaceae)

Analysis of the relationships among wild species of sectionMoutanin the plant genusPaeoniahas traditionally been problematic. Interspecies relationships cannot be effectively determined using phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast genome sequences will aid the identification and phylogeny of these species. In this study, the complete chloroplast genomes of three sect.Moutanplants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect.Moutanwere then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single copy (LSC) regions were considerably greater than those in the inverted repeat (IR) regions. Phylogenetic analysis revealed that the species of sect.Moutanclustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study,Paeonia jishanensisclustered with anotherP. jishanensissequence from the GenBank database,Paeonia qiuiclustered withPaeonia rockii, andPaeonia delavayivar.luteaclustered withPaeonia ludlowii. It was also found that the complete chloroplast genomes, LSC regions, and SSC regions all showed great abilities in identification and phylogenetic analysis of the species of sect.Moutan, while IRs regions and highly variable regions were not suitable for the species of sect.Moutan.