Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications

<p><em>Chamaerhodos</em> is a small genus with ca 7–8 species with a disjunct distribution in Asia and western North America. Due to limited sampling of species and genes in previous studies, little is known about the phylogenetic relationships among the species. Moreover, chloroplast genomic resources for <em>Chamaerhodos</em> have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five <em>Chamaerhodos</em> species. The five cp genomes had a typical quadripartite structure with high conservation of gene content and gene order. These five cp genomes encoded an identical set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparison of the boundaries between the IRs and single copy regions revealed only very slight boundary differences and the five cp genomes showed only little sequence divergence. Seven regions (<em>trnR-UCU-atpA</em>,<em> trnS-GCU- trnG-UCC</em>, <em>TrnG-GCC-trnfM-CAU</em>, <em>trnL-UAA</em> intron, <em>trnH-GUG-psbA</em>, <em>trnF-GAA- ndhJ</em>, <em>matK-5′-trnK-UUU</em>) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of <em>Ch. altaica</em>, <em>Ch. canescens</em>, <em>Ch. erecta</em>, <em>Ch. sabulosa</em> and <em>Ch. trifida</em>, respectively. A phylogenetic analysis support the monophyly of <em>Chamaerhodos</em> and place it as part of the Fragariinae clade sister to the clade of <em>Dasiphora</em>, <em>Drymocallis</em> and <em>Potaninia</em>. Within <em>Chamaerhodos</em>, <em>Ch. canescens</em> was inferred sister to a clade containing the other four species. The detailed characterization of the <em>Chamaerhodos</em> chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.</p>