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

Abstract

Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild <i>Fragaria</i> spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus <i>Fragaria</i> have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild <i>Fragaria</i> species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of <i>Fragaria</i> 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, <i>trnS</i>-<i>trnG</i>, <i>trnR</i>-<i>atpA</i>, <i>trnC</i>-<i>petN</i>, <i>rbcL</i>-<i>accD</i>, and <i>psbE</i>-<i>petL</i>, were identified that could be used to develop DNA barcoding for identification of <i>Fragaria</i> 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 <i>F. chiloensis</i> and <i>F. virginiana</i> and the tetraploid species <i>F. moupinensis</i> and <i>F. tibetica</i>. The complete cp genomes of these <i>Fragaria</i> spp. provide valuable information for selecting high-quality <i>Fragaria</i> germplasm resources in the future.