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Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild  Fragaria  spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus  Fragaria  have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild  Fragaria  species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of  Fragaria  was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci,  trnS - trnG ,  trnR - atpA ,  trnC - petN ,  rbcL - accD , and  psbE - petL , were identified that could be used to develop DNA barcoding for identification of  Fragaria  species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species  F. chiloensis  and  F. virginiana  and the tetraploid species  F. moupinensis  and  F. tibetica . The complete cp genomes of these  Fragaria  spp. provide valuable information for selecting high-quality  Fragaria  germplasm resources in the future.

Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae)