Complete Chloroplast Genomes Of Three Lamiaceae Medicinal Plants:Comparative And Evolutionary Analysis In Lamiaceae

Chloroplasts play a crucial role in sustaining plant life and are irreplaceable during the long evolutionary process of plants.Traditional Chinese medicine is the treasure of our nation.The quality of Chinese medicinal materials should be strictly controlled as the use of counterfeit medicinal materials severely impedes the development of traditional Chinese medicine.Chloroplasts have been widely used in genetic engineering,plant phylogeny and species identification owing to their unique structure and conservation.However,the chloroplast genomes of most medicinal plants have not been reported,which limits the use of chloroplast genomes for the identification of medicinal materials.This study focuses on the chloroplast genomes of three Lamiaceae medicinal plants Mentha haplocalyx Briq.,Ajuga decumbens Thunb.and Glechoma longituba(Nakai)Kupr,which can not only enrich the genetic information of these three species,but also promote the identification of Chinese medicinal materials.Through the extraction of chloroplast DNA,next-generation sequencing and bioinformatics methods,the complete chloroplast genomes of M.haplocalyx,A.decumbens and G.longituba are obtained.Then,we conducted comparative and evolutionary analysis in Lamiaceae.The main results are shown below:(1)The complete genomes of M.haplocalyx,A.decumbens and G.longituba are 152,050 bp,150,377 bp and 151,768 bp in length and all of them contain a circular quadripartite structure with a pair of inverted repeats(IR)separated by large(LSC)and small(SSC)single copy regions.They encode 80 protein-coding genes,30 tRNA genes and 4 rRNA genes.Further analysis includes the base composition,repeat structures and codon usage of these species,which contributes to the studies of optimal codons and molecular markers.(2)Comparative genomic analysis in Lamiaceae has been conducted using sequences extracted from NCBI.Sequence divergence has been analyzed and several hypervariable regions have been reported,which could be developed as potential molecular markers.Two small inversions are found conservative in Lamiaceae and their hairpin structures are predicted.The ratios of synonymous and nonsynonymous substitution rates of most genes are lower than 1,which suggest a purifying selection may act on them.(3)The phylogenetic relationship in Lamiaceae has been reconstructed using three methods.Three phylogenetic trees share the same structure and most nodes are strongly supported.The positions of M.haplocalyx,A.decumbens and G.longituba are strongly supported,which are consistent with former studies.This study reports the chloroplast genomes of three medicinal plants,which not only enriches the genetic data of medicinal plants,but also provides useful information for species identification and the utilization of DNA barcode.Meanwhile,this study further conducts comparative analysis and reconstructs the phylogenetic relationship in Lamiaceae,which may be helpful for molecular biology research in Lamiaceae.