Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three Medicinal Species for Bioexploration.

To systematically determine their phylogenetic relationships and develop molecular markers for species discrimination of , , and , we sequenced their chloroplast genomes using the Illumina Hiseq 2500 platform. The chloroplast genomes length of , , and were 151,387 bp, 150,604 bp, and 151,163 bp, respectively. The six genes B, 2, 23, 7, 12, and 2 were present in the IR regions. The chloroplast genomes of , , and contain 29 tandem repeats; 35, 29, 24 simple-sequence repeats, and 47, 49, 40 interspersed repeats, respectively. The three specific intergenic sequences (IGS) of 16-Q-UUG, L-UAA-F-GAA, and M-CAU-E were found to discriminate the 23 species. A total of 91 intergenic spacer sequences were identified through genetic distance analysis. The two specific IGS regions (G-GCCM-CAU and 3-S-GGA) have the highest K2p value identified in the three studied species. Furthermore, the phylogenetic tree showed that the 23 species formed a monophyletic group. Two pairs of genus-specific DNA barcode primers were found. The results will provide a solid foundation to understand the phylogenetic classification of the three species. Moreover, the specific intergenic regions can provide the probability to discriminate the species between the phenotype and the distinction of gene fragments.