Phylogenomics Study Of Carpesium(Asteraceae)

Carpesium has been widely recognized since it was established,and also been developed and utilized,especially in medicinal purposes.Though some researchs about systematic research have carried out on Carpesium,and the genetic relationship preliminarily discussed about some species of Carpesium,there are still many problems to be solved urgently,such as the unclear branch relationship in the genus and the genetic relationship of some species is still unclear.In addition,there are some problems existed in the previous molecular phylogenetic research results based on DNA fragments.They may be related to insufficient information sites for some DNA fragments,so these DNA fragments may be not suitable for the phylogenetic analysis in Carpesium.Based on some phylogenetic problems and some DNA fragments may not be suitable for the phylogenetic analysis in Carpesium,this study mainly carried out the phylogenetic research of this genus based on three kinds of data(DNA Fragments,Chloroplast Genomes,and dd-RAD).First,the DNA fragment data selected two most complete and frequently used fragments about Carpesium,including the latest published species.Based on the phylogenetic analysis results of these two DNA fragments,the applicability of the DNA fragments are verified about the phylogenetic analysis in Carpesium firstly,and then the phylogenetic relationship are preliminarily determined about Carpesium.Secondly,referring to some relevant phylogenetic genomics studies,this study combined the chloroplast genome and simplified genome data to conduct phylogenetic analysis of Carpesium,the result of which canverify the preliminary results based on DNA fragments.At the same time,by compared with the the whole chloroplast genome,some chloroplast fragments suitable for the systematic analysis of Carpesium can be screened out.After the phylogenetic tree was constructed bethe dd-RAD data,some key traits were combined for trait analysis.The analysis of the three kinds of data is mainly to solve the systematic problems of Tianmingjing,and also provide some other evidences.referring to related some phylogenetic genomics studies,this study used chloroplast genome and dd-RAD data to conduct phylogenetic analysis.At the same time,the chloroplast genome data was also used to screen out the chloroplast fragments suitable for the systematic analysis by the whole chloroplast genome compareing.After constructing a phylogenetic tree based on dd-RAD data,the trait analysis can be performed by combining some key traits.The analysis of the three kinds of data mainly solves the systematic problems of this genus,and provides some other evidences at the same time.The main results of the analysis based on three kinds datas are as follows:(1)The phylogenetic analysis based on the molecular fragment data of more species verified the inadequacy of DNA fragment-based,and identified the main clades of Carpesium.There are not clear 2 major clades,but 4 closely related clades about some species.;(2)Whole-genome sequencing of chloroplasts was performed on half speciess of the Carpesium,and then the interspecies relationships of some species were assessed at the chloroplast genome level.The results are mainly divided into two parts: on the one hand,the chloroplast genome structure shows that there are two different 4-division structures of the chloroplast genome map in Carpesium at firstly.The structure of Carpesium abrotanoides is different from other species of Carpesium,and it is closer to the species of Inula.Secondly,the IR boundary further verified that there are three cases in the chloroplast genome of Carpesium.C.abrotanoides was also more similar to that of Inula’ species.The rest species of Carpesium had other two cases about IR boundary.Finally,by analyzing the variation sites of the entire chloroplast genome,the chloroplast gene sequence suitable for the phylogenetic study of Carpesium was screened,and the reason why the phylogenetic analysis based on DNA fragmentswas isn’t good also verified.On the other hand,the phylogenetic analysis based on the entire chloroplast genome and common CDS sequences in the chloroplast genome provided a relatively stable and reliable result,identified some clades previously proposed based on fragment analysis,and also clarified the phylogenetic status of C.abrotanoides and C.leptopphyllum.;(3)dd-RAD sampling covers 70% of the species of Carpesium.The phylogenetic results of the 4 key traits of the 14 species were mutually verified with the previous results,and the phylogenetic relationship between C.rosulatum and C.glossophyllum were further verified.The ancestral traits analyzing of the 4 key traits screened out by principal component analysis of the 16 species,and to explore the evolution law about 4 key traits.The comprehensive results determine the system of Carpesium.