Analysis of the complete chloroplast genomes of and (Lamiaceae).

Linn. is a perennial herb with about 300 species. This genus has high medicinal value and many are used in Traditional Chinese Medicine (TCM). In this study, we sequenced and assembled the complete chloroplast genomes of and . Subsequently, we conducted a comprehensive comparative genomics analysis with 12 other published species. These genomes all had a conserved quartile structure, and the gene contents, gene sequences and GC contents are highly similar. The study on the genetic characteristics and nucleotide substitution rate of different genes found that the protein-coding genes of chloroplasts have differed greatly. Most genes are under purifying selection, but the 12 gene may have undergone positive selection. Besides, we identified three hypervariable regions as potential markers for taxa, which could play an important role in species identification of . Phylogenetic analysis showed that the 14 taxa were divided into two major clades. Moreover, the variation of IR regions is closely related to the evolutionary history as was reconstructed based on SNPs. In conclusion, we provided two high-quality chloroplast reference genomes of , this reliable information and genomic resources are valuable for developing of efficient DNA barcodes as reconstruction of chloroplast evolutionary history of the genus.