Phylogenetic relationships of Prunus (Rosaceae) in Korea and Japan inferred from chloroplast DNA sequences

We used sequences from both rbcL gene and trnL-trnF intergenic spacer of chloroplast DNA (cpDNA) for phylogenetic reconstruction of 39 accessions of Prunus distributed in Korea and Japan. No sequence length variation was found in the 39 accessions based on rbcL gene sequences. However, the length of the trnL-trnF spacer ranged from 358 to 387 base pairs (bp). Of the 1,790 aligned positions of the two cpDNA regions, 406 sites (22.7%) were variable: 299 sites (21.4%, 299/1,398) in rbcL and 107 sites (27.3%, 107/392) in the trnL-trnF intergenic spacer. The longest length mutation of the trnL-trnF spacer was a 21-bp deletion in P. padus and two taxa of P. buergeriana. Phylogenetic trees based on the sequence data were constructed by using maximum parsimony (MP) analysis. The bootstrap values for individual clades based on 1,000 replicates ranged from 80 to 100%. The strict consensus tree had five large, independent groups. The trees contained monophyletic groups consistent with the subgenera, Cerasus, Padus, Amygdalus, Prunophora, and Laurocerasus, with a common ancestral divergence point with a bootstrap value of 100%. In addition, subgenera Amygdalus and Prunophora had a well-supported sister group relationship with 100% bootstrap support, as did the clade of subgenera Cerasus, Laurocerasus and Padus. The two natives of P. yedoensis from Jeju, Korea were clearly distinguished from the cultivars as suggested in previous reports. Accordingly, cpDNA sequence analysis is a useful approach for reconstructing phylogenetic relationships among members of the genus Prunus distributed in Korea and Japan.