Complete chloroplast genome of <i>Prunus rufa</i> (Rosaceae), a wild flowering cherry endemic to the Himalayan region

<i>Prunus rufa</i> is a species of Prunus native to the Himalayan region. We determined the first complete chloroplast genome of <i>P. rufa</i> using a genome skimming approach. The cp genome was 157,723 bp long, with a large single-copy region (LSC) of 85,860 bp and a small single-copy region (SSC) of 19,081 bp separated by a pair of inverted repeats (IRs) of 26,391 bp each. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of <i>Prunus sensu lato</i> using maximum-likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that <i>P. rufa</i> is closely related to <i>Prunus cerasoides</i>.