Study On The Affinity And Evolution Of Eupatorieae Plants Based On Chloroplast Genome

The Eupatorieae is an annual or perennial herbaceous herb of the Asteraceae family,widely distributed in China and other Asian countries,and even on other continents.It is one of the common horticultural and medicinal plants with high ornamental and medicinal value.It has antibacterial,heat-clearing,detoxification,anti-cancer,antioxidant,and other effects.It’s taxonomy and phylogenetic relationships have long been controversial due to the lack of high-resolution molecular markers and new evolutionary insights,and research in this area is still lacking.To analyze the phylogenetic relationships and genetic background of the Eupatorieae,this study conducted high-throughput sequencing of the whole genome DNA of Eupatorium fortunei Turcz.,a plant of the Eupatorium genus.The basic genomic characteristics of chloroplast genome sequence structure,gene content and repetitive sequence of five genera including Eupatorium were analyzed.Comparative genomic analysis was performed on sequence similarity,nucleotide polymorphism,IR / SC boundary,and sequence collinearity.Based on the chloroplast genome data,the phylogenetic analysis and molecular marker development of the Eupatorieae were carried out.The main contents and results of this study are as follows:1.The first complete chloroplast genome sequence of the Eupatorium genus was obtained,with the NCBI sequence number OK545755.The chloroplast genome of E.fortunei,which is 152,401 bp in length and encodes 133 genes,has a typical quadripartite structure.The total length of the chloroplast genome ranging from 150,698 bp to 152,983 bp,and contains four characteristic regions of LSC,SSC and IRs(IRa and IRb).The length ranges are83,032 bp～84,829 bp,18,166 bp～34,967 bp and 30,902 bp～50,060 bp respectively.The overall GC content of the chloroplast genome is between 37.22 % to 37.63 %,and the total number of genes ranged from 124 to 136.The number of t RNA(Transfer RNA)and r RNA(Ribosomal RNA)in each group of each taxon of the Eupatorieae family was equal,37 and 8,respectively.2.A total of 588 SSR sequences and 1,000 long repeat sequences were identified in 20 Eupatorieae plants.The majority of the SSR sequences consisted of A/T mononucleotide repeats,while the long repeat sequences were mainly composed of forward and palindrome repeats.The codon usage of chloroplast genomes in the Eupatorieae plants is similar and generally prefers to end with A/T bases.There are 31 codons with RSCU > 1,with the codons encoding leucine,isoleucine,and serine having the highest frequency of usage,while the codons encoding methionine,tryptophan,and cysteine having the lowest frequency of usage.3.Nucleotide polymorphism,collinearity,and comparative genomics analyses of chloroplast genomes in the Eupatorieae species showed high collinearity among the 20 chloroplast genome sequences,with minor differences observed.The reverse repeat region IR was more conserved,and most mutations occurred in the non-coding region.Compared to other groups,the species of Ageratina adenophora in the Eupatorium genus and Mikania brevifaucia in the Mikania genus exhibited IR contraction.The boundary genes of SSC/IRa,LSC/IRb,SSC/IRb,and IRa/LSC were consistent.4.Based on the chloroplast genome sequences of the Eupatorieae species,two datasets were constructed-51 shared protein-coding gene CDS sequences and 19 protein-coding gene CDS sequences with an ω value of 1,selected by analysis of selection pressure.A phylogenetic tree for the five classification groups of the Eupatorieae was constructed,and a consistent topology with high branch support was observed.Two plants,A.adenophora and A.fastigiata,originally classified in the Eupatorium genus,were reclassified into the Ageratina genus.The Eupatorium genus was found to be more closely related to the Mikania genus,while the Ageratina and Mikania genera were sister groups.Based on various bioinformatics and comparative genomic analyses,including 22 highly variable regions such as ycf1,mat K,and psb M,potential molecular markers for identifying and locating Eupatorieae plants were identified,providing more objective evidence for their identification and classification.This study provides new evidence for the classification,phylogeny,and molecular marker development of Eupatorieae plants,promoting their identification,research,and conservation.