Comparative analysis of chloroplast genome in medicinal plants of Elsholtzia and E.fruticosa
[Objective]In order to comprehensively analyze the complete chloroplast genome sequence and structural characteristics of Elsholt-zia fruticosa,the article discussed the overall characteristics and variation patterns of the chloroplast genome of the medicinal plant Elsholt-zia.The interspecific variation of the sequence was compared and the high variation sequence was screened,which laid a foundation for the in-depth study and application of the chloroplast genome of Elsholtzia medicinal plants.[Method]The chloroplast genome of the traditional ethnomedicinal plant E.fruticosa was sequenced,assembled,and annotated using high-throughput sequencing technology.At the same time,softwares such as MISA-web were used to analyze the IR limit,codon usage preference parameters,nucleotide composition and evolu-tionary relationship of the chloroplast genome of four Elsholtzia medicinal plants(E.fruticosa,E.splendens,E.densa,E.byeonsanensis).[Result](ⅰ)The total length of the chloroplast genome was 151 550 bp,with a typical tetrad structure and 49 simple sequence repeats(SSRs)detected.(ⅱ)The expansion and contraction of the chloroplast genome boundary of the four medicinal plants of Elsholtzia were rela-tively stable and similar,and only small variations had occurred in individual species(E.splendens,E.byeonsanensis).(ⅲ)The differ-ences between the non-coding regions of the four Elsholtzia medicinal plants were greater than that of the coding region.At the same time,the large single copy region(LSC)had the highest degree of variation,and the inverted repeat region(IRa)had the lowest degree of varia-tion.(ⅳ)Compared with the other three species,the chloroplast genome of E.fruticosa had the lowest degree of variation.There were sig-nificant differences in the coding regions of psbA,petA,psbF,ycf1,petG and psbL.At the same time,intergenic regions such as trnQ-UUG,trnS-GCT,trnM-GTT,trnS-GGA,and trn.L-CAA also showed varying degrees of variation.(ⅴ)Codon bias in the chloroplast genomes of four medicinal plants of Elsholtzia was mainly affected by base mutations and selection pressure.Most of the optimal codons were A or T(U)as the third base.(ⅵ)The phylogenetic tree showed that the genetic relationship between E.fruticosa and E.rugulosa was the closest.[Con-clusion]The study provides a reference for the phylogenetic study and molecular marker development of Elsholtzia medicinal plants.
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