Chamaerhodos 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 Chamaerhodos have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five Chamaerhodos 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 (trnR-UCU-atpA, trnS-GCU- trnG-UCC, TrnG-GCC-trnfM-CAU, trnL-UAA intron, trnH-GUG-psbA, trnF-GAA- ndhJ, matK-5′-trnK-UUU) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of Ch. altaica, Ch. canescens, Ch. erecta, Ch. sabulosa and Ch. trifida, respectively. A phylogenetic analysis support the monophyly of Chamaerhodos and place it as part of the Fragariinae clade sister to the clade of Dasiphora, Drymocallis and Potaninia. Within Chamaerhodos, Ch. canescens was inferred sister to a clade containing the other four species. The detailed characterization of the Chamaerhodos chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.

Figure S1. MAUVE alignments of chloroplast genomes of five Chamaerhodos species.

Table S1. The GenBank accession numbers of all the 41 chloroplast genome sequences used for phylogenetic analysis.

Table S2. The nucleotide diversity (Pi) values of 264 homologous loci.