Comparative analysis of chloroplast genomes of endangered heterostylous species and its closely related species.

, well known for its heterostyly, is the largest genus in the family Primulaceae with more than 500 species. The considerable species number has introduced a huge challenge for taxonomy. The phylogenetic relationships among still maintain unresolved due to frequent hybridization and introgression between closely related species. In this study, we sequenced and assembled the complete chloroplast genomes of Dunn, which is a PSESP (plant species with extremely small populations), using Illumina sequencing and compared its genomic sequences with those of four related species. The chloroplast genomes of species were similar in the basic structure, gene order, and GC content. The detected 38 SSRs (simple sequence repeats) loci and 17 hypervariable regions had many similarities in , , , and , but showed a significant difference compared with those in . Slight variations were observed among chloroplast genomes, in consideration of the relatively stable patterns of IR (inverted repeats) contraction and expansion. Phylogenetic analysis based on chloroplast genomes and protein-coding genes confirmed three major clades in Chinese , but the infrageneric sections were not in accordance with morphological traits. The complex was confirmed here and was the most closely related species to . Overall, the chloroplast genome sequences provided useful genetic and evolutionary information for phylogeny and population genetics on Chinese species.