Characterization of the Complete Chloroplast Genome of the Dragonhead Herb, <i>Dracocephalum</i><i>heterophyllum</i> (Lamiaceae), and Comparative Analyses with Related Species

<i>Dracocephalum heterophyllum</i> (Lamiaceae: tribe Mentheae) is an annual aromatic herb native to East Asia with a long record of human uses, including medicinal, alimentary, and ornamental values. However, no information is available about its molecular biology, and no genomic study has been performed on <i>D</i><i>. heterophyllum</i>. Here, we report the complete chloroplast (cp) genome of <i>D.</i> <i>heterophyllum</i> and a series of comparative genomic analyses between this and closely related species of Lamiaceae. Results indicated that the cp genome has a typical circular structure of 150,869 bp in length, consisting of a long single-copy (LSC) region with 82,410 bp, a short single-copy (SSC) region with 17,098 bp, and two inverted repeat (IR) regions of 51,350 bp. A total of 133 genes were identified, including 37 tRNA genes, 8 rRNA genes and 88 protein-coding genes, with a GC content of 37.8%. The gene content, organization, and GC values observed here were similar to those of other <i>Dracocephalum</i> species. We detected 99 different simple sequence repeat loci, and the codon usage analysis revealed a preferential use of the Leu codon with an A/U ending. Comparative analysis of cp genome sequences revealed five highly variable regions with remarkably higher Pi values (>0.03). The mean <i>K</i>a/<i>K</i>s between <i>D. heterophyllum</i> and three other <i>Dracocephalum</i> species ranged from 0.01079 (<i>psbB</i>) to 1.0497 (<i>ycf2</i>). Two cp genes, <i>ycf2</i> and <i>rps11</i>, were proven to have high ratios of <i>K</i>a<i>/K</i>s, implying that cp genes may had undergone positive selection in the evolutionary history. We performed multiple sequence alignments using the cp genome of 22 species and constructed maximum likelihood (ML) and Bayesian trees, and found that <i>D</i><i>. heterophyllum</i> were more closely related to <i>D. moldavica</i> and <i>D. palmatum</i>. In addition, the phylogenetic relationships between <i>Dracocephalum</i> and other members of Lamiaceae were consistent with previous results. These results are valuable for further formulating effective strategies of conservation and management for species in <i>Dracocephalum</i>, as well as providing a foundation for future research on the genetic resources of <i>Dracocephalum</i>.