Comparative Analysis of Complete Chloroplast Genomes of in China: Hypervariable Regions and Phylogenetic Relationships.

With more than 200 species of native , China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese species (including varieties) from three of the eight sections reported in China, i.e., the sections , , and . Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: , , , , , , intron, , and . Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these species. All sampled species formed a monophyletic group; however, sections and were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within .