Comparative plastomic analysis and insights into the phylogeny of (Lamiaceae).

is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. subg. , native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of (14 newly sequenced and 5 previously published). Our comparative analysis showed that all plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of are highly conserved, and IR contraction only occurred in two species ( and ). In , sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of , suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of , resolving the interspecific relationship of subg. . The newly sequenced plastid genomes will also enrich the plastome database of , providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.