AUTHOR=Wu Liwei , Nie Liping , Xu Zhichao , Li Pei , Wang Yu , He Chunnian , Song Jingyuan , Yao Hui 

TITLE=Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae)

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00980

DOI=10.3389/fgene.2020.00980

ISSN=1664-8021

ABSTRACT=<p>Analysis of the relationships among wild species of section <italic>Moutan</italic> in the plant genus <italic>Paeonia</italic> has 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. <italic>Moutan</italic> plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect. <italic>Moutan</italic> were 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. <italic>Moutan</italic> clustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study, <italic>Paeonia jishanensis</italic> clustered with another <italic>P. jishanensis</italic> sequence from the GenBank database, <italic>Paeonia qiui</italic> clustered with <italic>Paeonia rockii</italic>, and <italic>Paeonia delavayi</italic> var. <italic>lutea</italic> clustered with <italic>Paeonia ludlowii</italic>. 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. <italic>Moutan</italic>, while IRs regions and highly variable regions were not suitable for the species of sect. <italic>Moutan</italic>.</p>