title: Identification of three new isolates of Tomato spotted wilt virus from different hosts in China: molecular diversity, phylogenetic and recombination analyses.
abstract: BACKGROUND
  Destructive diseases caused by Tomato spotted wilt virus (TSWV) have been reported associated with many important plants worldwide. Recently, TSWV was reported to infect different hosts in China. It is of value to clone TSWV isolates from different hosts and examine diversity and evolution among different TSWV isolates in China as well as worldwide.
  
  
  METHODS
  RT-PCR was used to clone the full-length genome (L, M and S segments) of three new isolates of TSWV that infected different hosts (tobacco, red pepper and green pepper) in China. Identity of nucleotide and amino acid sequences among TSWV isolates were analyzed by DNAMAN. MEGA 5.0 was used to construct phylogenetic trees. RDP4 was used to detect recombination events during evolution of these isolates.
  
  
  RESULTS
  Whole-genome sequences of three new TSWV isolates in China were determined. Together with other available isolates, 29 RNA L, 62 RNA M and 66 RNA S of TSWV isolates were analyzed for molecular diversity, phylogenetic and recombination events. This analysis revealed that the entire TSWV genome, especially the M and S RNAs, had major variations in genomic size that mainly involve the A-U rich intergenic region (IGR). Phylogenetic analyses on TSWV isolates worldwide revealed evidence for frequent reassortments in the evolution of tripartite negative-sense RNA genome. Significant numbers of recombination events with apparent 5' regional preference were detected among TSWV isolates worldwide. Moreover, TSWV isolates with similar recombination events usually had closer relationships in phylogenetic trees.
  
  
  CONCLUSIONS
  All five Chinese TSWV isolates including three TSWV isolates of this study and previously reported two isolates can be divided into two groups with different origins based on molecular diversity and phylogenetic analysis. During their evolution, both reassortment and recombination played roles. These results suggest that recombination could be an important mechanism in the evolution of multipartite RNA viruses, even negative-sense RNA viruses.
authors.affiliation: College of Plant Protection, Shandong Agricultural University, No 61, Daizong Street, Tai'an, 271018, Shandong Province, P. R. China. zhangzhenjia2013@126.com.
authors.forename: Zhenjia
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: College of Plant Protection, Shandong Agricultural University, No 61, Daizong Street, Tai'an, 271018, Shandong Province, P. R. China. wangdeyasdny@163.com.
authors.forename: Deya
authors.initials: D
authors.lastname: Wang
authors.affiliation: College of Plant Protection, Shandong Agricultural University, No 61, Daizong Street, Tai'an, 271018, Shandong Province, P. R. China. ycm2006.apple@163.com.
authors.forename: Chengming
authors.initials: C
authors.lastname: Yu
authors.affiliation: College of Plant Protection, Shandong Agricultural University, No 61, Daizong Street, Tai'an, 271018, Shandong Province, P. R. China. wuhenbeijixiong@163.com.
authors.forename: Zenghui
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Resources Institute, Yunnan Academy of Agricultural Sciences, Yunnan Provincial Key Lab of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming, 650223, China. dongjhn@126.com.
authors.forename: Jiahong
authors.initials: J
authors.lastname: Dong
authors.affiliation: College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, P. R. China. krshi@sdau.edu.cn.
authors.forename: Kerong
authors.initials: K
authors.lastname: Shi
authors.affiliation: College of Plant Protection, Shandong Agricultural University, No 61, Daizong Street, Tai'an, 271018, Shandong Province, P. R. China. snowpeak77@163.com.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Yuan
mesh_terms: D002681:China; D014644:Genetic Variation; D016679:Genome, Viral; D018551:Solanum lycopersicum / Q000821:virology; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D016865:Reassortant Viruses / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014026:Nicotiana / Q000821:virology; D017865:Tospovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D014771:Virion / Q000648:ultrastructure