Phylogenetic analysis of Lamiaceae based on transcriptome data

Abstract

The Lamiaceae family is included in the angiosperms and comprises over 7000 species, many of which are of considerable ecological, economic, and cultural importance. We seek to establish a taxonomic basis by examining the speciation timeline in Lamiaceae using phylogenetics and publicly available transcriptome data. Since Ks is steadily accumulated over time in plants for environmental adaptation until speciation occurs, the timing of speciation can be estimated from examination of Ks values. A total of 24 species included in the Lamiaceae family used in our analysis belongs to four subfamilies. We performed transcriptome assembly for each of the 24 species using trimmed data collected from public databases. We compiled groups of gene families in which at least one copy of the gene is present in each species from orthologous groups among unigenes. From these groups, we obtained a total of 450,014 single nucleotide polymorphisms (SNPs) across 27 species, incorporating three additional outgroup species. Subsequently, a tree was created using these SNPs. In our tree, the outgroup species were clearly located externally, confirming the proximity of species within the same subfamily. The Ks peak corroborated the outcomes observed in the phylogenetic tree. We estimated the rate of sequence evolution and divergence time for each species on the phylogenetic tree by referencing the time of divergence among the Lamiaceae family. In particular, Clinopodium serpyllifolium, Lavandula × intermedia, Phlomis fruticosa, and Volkameria inermis were analyzed for the first time. Our study helps with the understanding of the function of plants included in the Lamiaceae family and is expected to provide a fundamental resource that can be used to pinpoint the molecular and genomic evolution of the Lamiaceae family.