Comparative analyses of Agrimonia complete chloroplast genomes with newly assembled chloroplast genomes of A. coreana and A. nipponica (Rosaceae)

The genus Agrimonia L. (1753) is a small group consisting of 19 species and three varieties. We completed two Agrimonia chloroplast genomes, Agrimonia coreana Nakai and Agrimonia nipponica Koidz, collected in Korea and conducted comprehensive analyses of six Agrimonia chloroplast genomes. Two of the Agrimonia chloroplasts genomes have a typical quadripartite structure with lengths ranging from 155,161 bp to 151,362 bp, similar to the remaining Agrimonia chloroplast genomes. High nucleotide diversity was detected in the ycf1 gene, which can serve as a molecular marker. Intraspecific variations of four A. pilosa chloroplast genomes and interspecific variations of three Agrimonia species revealed that KY419942 is distinct to the other three A. pilosa chloroplast genomes. A phylogenetic analysis demonstrated that KY419942 was clustered with A. nipponica, requiring further analyses to understand Agrimonia species in East Asia. A comparison of simple sequence repeats identified from the six Agrimonia chloroplast genomes suggests potential molecular markers to distinguish species or populations of the same species. Our results define the phylogenetic relationship of three Agrimonia species and provide insight into the intraspecific features of Agrimonia chloroplast genomes with which to gain a better understanding of the genetic structure of Agrimonia species.