Sequence Analysis And Phylogenetic Relationships Of Chloroplast Genome Of Coptis

Coptis is a perennial herbaceous plant of Ranunculaceae,with about 14 species,mainly distributed in the northern temperate zone,most of which are produced in eastern Asia.The underground rhizomes of Coptis is often used as Chinese medicinal materials and is listed as top-grade in "Shen Nong’s Materia Medica".It has the effects of clearing heat and dampness,reducing fire and detoxification,and has high economic value and good market prospects.At present,the market for Chinese medicinal materials is rather chaotic,with good and bad product quality coexisting,and adulteration is common.In order to ensure the safety of medication and people’s health,the technology of authenticity identification and quality testing of Chinese medicinal materials has attracted more and more attention and research from scholars.In previous studies,the identification of Coptidis mainly focused on morphological identification and active substance detection,which has the characteristics of high sample requirements,long time and artificial results.Molecular identification has the advantages of accuracy,speed,and low cost,and has become a common method and research hotspot in the field of identification.The chloroplast is an important organelle in plant cells,and its genome has high sequence conservation and low base substitution rate.Therefore,the study of the chloroplast genome facilitates the screening of highly variable sequence fragments of this genus,and is a powerful tool for studying species identification and phylogenetic development.In this study,we assembled and annotated the chloroplast genomes of six plants,Coptis chinensis var.brevisepala(MT773634),Coptis deltoidea(MT576696),Coptis omeiensis(MT773636),Coptis japonica(MT773635),Coptis Teeta(MT773638),and Coptis quinquesecta(MT773637).The final genome sequences were submitted to the NCBI official website.The genome sequence of Coptis chinensis(MK569483.1)was also downloaded.Using bioinformatics technology,the chloroplast genomes of 7 species of Coptis were compared,the sequence fragment identification ability was evaluated and phylogenetic analysis of the genus was carried out.Finally,this article provides data support for further in-depth research on the chloroplast genome of this genus,provides new ideas for species identification,and provides a research basis for phylogenetic development.The main contents and results of this research are as follows:(1)The chloroplast genomes of seven species of Coptis showed a tetrad structure(LSC/IRa/SSC/IRb),and the length of each species was slightly different(154,156 bp-154,985 bp).The chloroplast genome encoded 131 genes,including 86 protein-coding genes,37 t RNA genes and 8 r RNA genes.Among them,the 23 intron-containing genes contained 27 introns,including rps12,a trans-splicing gene.The number of codons of protein-coding genes was less varied(26,494-26,652).The amino acid that encodes the most is leucine and the least is cysteine.The RSCU values encoded by protein coding genes are similar,with 31 preferred codons(RSCU>1).The chloroplast genomes have identified a total of 65 direct repeats,77 tandem repeats and 97 palindromic repeats.In addition,single nucleotide SSR(1004),dinucleotide SSR(96),trinucleotide SSR(41),tetraducleotide SSR(60),pentucleotide SSR(5),and hexnucleotide SSR(4)were also identified.In addition,there were minor differences in the chloroplast genomes of the seven species of Coptis at the IR/SC boundary.(2)The sequence similarity analysis of the chloroplast genomes of seven species of Coptis showed that there were differences.The coding region was more conservative than the non-coding region,and the nucleotide polymorphism in the IR region was significantly lower than that in LSC region and SSC region.The ycf1 gene has multiple mutation sites and was a highly variable gene.In this study,trn H-GUG-psb A、pet A-psb J、ccs A-ndh D and ndh F-rpl32 with the highest mutation rate and moderate length were recommended as the specific DNA barcodes of Coptiana plants.Phylogenetic analysis showed that all seven Coptis species clustered together and fprm a monophyletic group.In our phylogenetic trees(ML tree and NJ tree),Coptis quinquesecta was the most basic,followed by Coptis japonica,Coptis teeta and Coptis omeiensis.Coptis deltoidea,Coptis chinensis var.Brevisepala and Coptis chinensis are closely related.