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

Abstract

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