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