Complete chloroplast genome of cultivated flowering cherry, Prunus ×yedoensis ‘Somei-yoshino’ in comparison with wild Prunus yedoensis Matsum. (Rosaceae)

Prunus ×yedoensis Matsum. ‘Somei-yoshino’ is the most common and widespread cultivar of the ornamental flowering cherries. We hereby report its complete chloroplast (cp) genome sequences generated by whole-genome next-generation sequencing approach. The cp genome size was 157,792 bp in length consisting of four regions; large single-copy region (85,914 bp), small single-copy region (19,120 bp), and a pair of inverted repeat regions (26,379 bp). The genome contained a total of 131 genes, including 86 coding genes, 8 rRNA genes, and 37 tRNA genes. A total of 92 simple sequence repeats (SSRs) were detected within the cp genome. Its molecular features were compared with the complete cp genome of wild P. yedoensis, which occurs rarely in natural habitats of Mt. Halla in Jeju Island, Korea, displaying nearly indistinguishable morphology as P. ×yedoensis ‘Somei-yoshino’. Although both cp genomes were structured highly alike, the sequence variations between them were revealed in several single-nucleotide polymorphisms (SNPs). Using additional individuals of wild and cultivated flowering cherries, PCR amplification confirmed that those SNPs were phylogenetically informative, providing distinction between wild and cultivated flowering cherries. In future study, the SNPs and SSRs reported in this study could be used to identify wild individuals from morphologically identical cultivars of flowering cherries and also to conserve the genetic diversity of wild flowering cherries in Jeju Island.