Research On Chloroplast Genome Structure And Phylogenetic Relationships Of Eupatorium Adenophorum

Eupatorium adenophorum Spreng, plant belongs to genus Eupatorium, family Asteraceae. It is a rapidly spreading, invasive exotic weed. It has invaded around 30 countries in tropical and subtropical zones. E. adenophorum has caused serious economic losses and threatened native biodiversity and even affected health of humans and livestock. In the invasion process, its habitat conditions have dramatically changed, reflecting its strong adaptability. In this study, we analyzed the phylogeny of E. adenophorum based on both chloroplast and nuclear DNA. Our aim is to provide a theoretical basis for the the mechanism of invasion and population genetics; it may also lay a foundation for the development of biological invasions. The main results of our research are as follows:(1) In order to analyze the taxonomic status of E. adenophorum in Asteracea,the three chloroplast sequences of E. adenophorum were amplified by PCR and sequenced. All the sequences were aligned with other chloroplast genes of Asteracea species, available at NCBI. Phylogenetic analysis was done using Mega 4. 0 Software. Phylogenetic relationships were estimated by neighbor-joining method. The results showed that Eupatorium adenophorum Spreng has the closest taxonomic status with the other plants of genus Eupatorium and Guizotia abyssinica where as Chrysanthemum indicum, Leucanthemum vulgare and Lactuca sativa are far relatives. So our molecular evidences indicate that Eupatorium adenophorum Spreng belongs to the genus Eupatorium; the sequences of the combined dataset ranged from 2,140 to 2,203 bp in length and the aligned sequences length were 2,399 bp in length,which included 381 variable sites and 190 parsim- info sites. Analyses of three separate and combined datasets provided a good amount of informative characters and resolved the systematical relationships of E. adenophorum as well.(2) We obtained the complete chloroplast (cp) genome sequences of Eupatorium adenophorum by Solexa sequencing technology. The Eupatorium adenophorum chloroplast genome is 150,698 bp in length which includes a pair of inverted repeats (IRs) of 23,756 bp separated by a small single-copy region of 18,358 bp and a large single-copy region of 84,828 bp. The GC content of the chloroplast genome is 37.46%. The genome contains 112 unique genes. Of these, 80 are predicted protein-coding genes, 4 ribosomal RNA genes and 28 tRNA genes. 19 of 112 genes are duplicated in the IR, so the total number of genes is 131. 16 genes contains introns, of which 3 genes have two introns respectively. Total 13 genes were found to contain an intron, 5 genes are in the IR region. The length of CDS is 74682 bp, encoding 24,894 amino acids. The chloroplast genome of Eupatorium adenophorum has the similar contents and orders with other Asteraceae: Helianthus annuus, Guizotia abyssinica, Lactuca sativa and Parthenium argentatum. When compared to tobacco, these genomes have two inversions: a large about 23-kb inversion and a smaller 3.4-kb inversion nested within it. Based on the overall comparison of the cpDNA with L. sativa, G. abyssinica , H. annuus, P. argentatum by zPicture software, we demonstrate that the E. adenophorum chloroplast genome sequence is most closely related to that of G. abyssinica. Pairwise sequences divergence across all coding genes in Helianthus has resulted in the discovery of fast-evolving DNA sequences for use in phylogenetics, such as the ndhK、ycf1 and accD genes. The NJ phylogenetic tree is based on 35 protein-coding genes from 31 plant taxa using Mega 4.0 version. Phylogenetic analysis demonstrated a close relationship between E. adenophorum and other Asteraceae and provided a strong support for a group of the euasterids II.(3) In previous studies, no one has found suitable SSR markers for Eupatorium adenophorum. We selected 21 microsatellites from nucleus DNA by high throughput sequencing and then designed and tested primers for their amplifications by 10 Strains. 15 pairs of SSR markers were polymorphic and 1 pair of primers S6- 137 can not have a clear target amplified bands. The other five pairs of primers did not amplify the polymorphism. Polymorphism of SSR markers we designed in E. adenophorum is low. May be the possible reasons are: the development of polymorphic SSR markers is low; the materials are less genetic variations because of close locations.