title: Genetic diversity and population structure of rice stripe virus in China.
abstract: Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997-2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Tai-Yun
authors.initials: TY
authors.lastname: Wei
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Jin-Guang
authors.initials: JG
authors.lastname: Yang
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Fu-Long
authors.initials: FL
authors.lastname: Liao
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Fang-Luan
authors.initials: FL
authors.lastname: Gao
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Lian-Ming
authors.initials: LM
authors.lastname: Lu
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Xiao-Ting
authors.initials: XT
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Agricultural Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, PR China.|Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Fan
authors.initials: F
authors.lastname: Li
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Zu-Jian
authors.initials: ZJ
authors.lastname: Wu
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Qi-Yin
authors.initials: QY
authors.lastname: Lin
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Lian-Hui
authors.initials: LH
authors.lastname: Xie
authors.affiliation: Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, PR China.
authors.forename: Han-Xin
authors.initials: HX
authors.lastname: Lin
mesh_terms: D002681:China; D003001:Cloning, Molecular; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D012275:Oryza / Q000821:virology*; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D029364:Tenuivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins