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.