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

Primula, 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. Although several phylogenetic constructions have been carried out thoroughly, the relationships between Primula species were remained incompletely understood, especially for the relationship among sections within Chinese species. P. wilsonii Dunn is a PSESP (plant species with extremely small populations) with very limited genetic information to explore its endangered mechanism and conservation. In this study, we sequenced and assembled the complete chloroplast genomes of P. wilsonii using Illumina sequencing and compared its genomic sequences with those of four related Primula species. The chloroplast genomes of Primula species were similar in the basic structure, gene order and GC content. The detected 38 SSRs loci and 17 hyper-variable regions had many similarities in P. wilsonii, P. anisodora, P. miyabeana and P. poissonii, but showed a significant difference compared with those in P. secundiflora. Slight variations were observed among Primula chloroplast genomes, in consideration of the relatively stable patterns of IR contraction and expansion. Phylogenetic analysis based on chloroplast genomes confirmed three major clades in Chinese Primula, but the infrageneric sections were not in accordance with morphological traits. The P. poissonii complex was confirmed here and P. anisodora was the species that was most closely related to P. wilsonii. Overall, the chloroplast genome sequences provided useful genetic and evolutionary information for phylogeny, population genetics and conservation studies on Chinese Primula species.