V. bicolor, V. trifolia s. str. and V. rotundifolia are part of a species complex that has recorded medicinal use in the Philippines. We assembled the first chloroplast genome of V. bicolor through next-generation sequencing and compared this to earlier established chloroplast genomes of V. trifolia s. str. and V. rotundifolia to provide additional insights into their genotypic differences. To ensure the continued utility of the research outputs in case of future taxonomic revisions, we characterized the morphology of PBN 2018-674, the reference germplasm utilized to generate the plastome. The complete chloroplast genome sequence of V. bicolor was 154,460 bp long with 131 coding genes comprising 87 mRNA genes, 36 tRNA genes and 8 rRNA genes. Using a separate accession from a different type locality, an identical chloroplast genome was equally established, indicating its conserved nature. When compared to V. trifolia s. str. and V. rotundifolia, slight variations were observed in genome features between these species; however, single nucleotide polymorphisms were exhibited in 13 protein-coding genes that often have a conserved nature. A phylogenetic analysis of the assembled genome, together with 12 other Lamiaceae species, exhibited high bootstrap support (>88%) within the species complex, and associated V. trifolia as the closest relative of V. bicolor. The identified variations in the plastomes can be utilized as markers that could distinguish the three closely related genotypes which can help the Philippine herbal industry provide a more stable source of quality herbal medicines.
