Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

Abstract Background Prunus Cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. Cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast (cp) genome of P. Cistena and compared it with related species of Prunus genus based on chloroplast genome. Results The complete chloroplast genome of P. Cistena was 157,935 bp in length, which had a typical tetrad structure. The overall GC content was 36.72%, while IR regions displayed a higher GC content than LSC and SSC regions. It encoded 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes had two introns; the longest intron was trnK-UUU gene in the LSC region. There were 253 SSRs, and the mononucleotide SSRs were the most abundant. The chloroplast sequences and gene arrangements of P. Cistena were conserved, which overall structure and gene order were similar to other Prunus species. The atpE , ccsA , petA , r ps8 and matK gene had significant positive selection in Prunus species. P. Cistena had a close evolutionary relationship with the P. jamasakura . The coding region and IR region were more conserved than noncoding region, and the cpDNA sequences highly conserved throughout the genus Prunus . Conclusions The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of genus Prunus .