Sequence Characteristics and Phylogenetic Analysis of the Chloroplast Genome.

Levl. et Van is an important species with a high medicinal value. There are abundant germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of in the family are still unclear. In this study, the chloroplast (cp) genomes of 72 varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 species were found to be significantly different. A sequence divergence analysis of cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 species. The resulting tree was consistent with the traditional classification system; species were clustered into one group, and was shown to be closely related to and . In summary, this study systematically analyzed the cp genome characteristics of and compared cp genomes of species. The results provide valuable information for the definitive identification of varieties and for the understanding of the evolutionary relationships between species.