Whole Chloroplast Genome and Sequence Variation in the Family Lamiaceae

The Lamiaceae family, a large and cosmopolitan group comprising 236 genera and over 7,000 species, is primarily found in the Mediterranean basin and Central Asia. This family is characterized by bilabiate corollas, epipetalous or didynamous stamens, verticillaster flowers, and schizocarp fruits. In this study, we analyzed the complete chloroplast (cp) genome sequences of 51 species to explore the evolutionary trends and phylogenetic relationships within the Lamiaceae family. The complete chloroplast genome is valuable for studying sequence divergence, phylogenomics, and molecular evolution. We characterized the chloroplast genome structure, including gene number and order, simple sequence repeats (SSRs), and the variety and distribution of large repeat sequences. The cp genome sizes of Lamiaceae species ranged from 149,095 bp (Elsholtzia densa) to 154,495 bp (Vitex agnus-castus). The large single copy (LSC) region varied from 81,610 bp (Alyssum gmelinii) to 84,907 bp (Lamium album), the small single copy (SSC) region from 17,621 bp (Ajuga nipponensis) to 26,234 bp (Origanum vulgare), and the inverted repeats (IRs) ranged from 26,051 bp (Origanum vulgare) to 26,890 bp (Salvia officinalis). These genomes consist of circular DNA molecules, similar to those found in most angiosperms. The complete cp genomes of Lamiaceae species contain between 80 and 134 functional genes, including 84–89 protein-coding genes, 8 rRNA genes, and 35–39 tRNA genes. Among the 50 plastomes, the highest GC content (38.7%) was observed in Stachys byzantina and Leonotis leonurus, while the lowest GC content (37.7%) was found in Coleus hadiensis, Coleus xanthanthus, and Coleus scutellarioides. We identified three main types of repeat sequences: dispersed, palindromic, and tandem. A total of 5,349 repeat elements were identified, with palindromic repeats being the most abundant (2,895; 55%), followed by tandem repeats (1,528; 28%) and dispersed repeats (926; 17%). Ultimately, the phylogenetic analysis revealed that the 50 Lamiaceae species are closely related, providing critical insights into the sequence variation, phylogenetic connections, and molecular evolution of Lamiaceae plastid genomes.