title: The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates.
abstract: Soybean mosaic virus (SMV) is widely recognized as a highly damaging pathogen of soybean, and various strains/isolates have been reported to date. However, the pathogenic differences and phylogenetic relationships of these SMV strains/isolates have not been extensively studied. In the present work, by first obtaining 18 new genomic sequences of Chinese SMV strains/isolates and further compiling these with available data, we have explored the evolution of SMV from multiple aspects. First, as in other potyviruses, recombination has occurred frequently during SMV evolution, and a total of 32 independent events were detected. Second, using a maximum-likelihood method and removing recombinant fragments, a phylogeny covering 83 SMV sequences sampled from all over the world was reconstructed and the results showed four separate SMV clades, with clade I and II recovered for the first time. Third, the population structure analysis of SMV revealed significant genetic differentiations between China and two other countries (Korea and U.S.A.). Fourth, certain SMV-encoded genes, such as P1, HC-Pro and P3, exhibited higher non-synonymous substitution rate (dN) than synonymous substitution rate (dS), indicating that positive selection has influenced these genes. Finally, four Chinese SMV strains/isolates were selected for inoculation of both USA and Chinese differential soybean cultivars, and their pathogenic phenotypes were significantly different from that of the American strains. Overall, these findings have further broadened our understanding on SMV evolution, which would assist researchers to better deal with this harmful virus.
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Guang-Can
authors.initials: GC
authors.lastname: Zhou
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Zhu-Qing
authors.initials: ZQ
authors.lastname: Shao
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Fang-Fang
authors.initials: FF
authors.lastname: Ma
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Wu
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Xiao-Yi
authors.initials: XY
authors.lastname: Wu
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
authors.forename: Zhong-Yun
authors.initials: ZY
authors.lastname: Xie
authors.affiliation: National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing 210095, China.
authors.forename: De-Yue
authors.initials: DY
authors.lastname: Yu
authors.affiliation: National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing 210095, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Cheng
authors.affiliation: College of Resources and Environment, Northeast Agriculture University, Harbin 150030, China.
authors.forename: Zhi-Hua
authors.initials: ZH
authors.lastname: Liu
authors.affiliation: College of Agriculture, Northeast Agriculture University, Harbin 150030, China.
authors.forename: Zhen-Feng
authors.initials: ZF
authors.lastname: Jiang
authors.affiliation: College of Agriculture, Northeast Agriculture University, Harbin 150030, China.
authors.forename: Qing-Shan
authors.initials: QS
authors.lastname: Chen
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China. Electronic address: binwang@nju.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China. Electronic address: chenjq@nju.edu.cn.
authors.forename: Jian-Qun
authors.initials: JQ
authors.lastname: Chen
mesh_terms: D002681:China; D019143:Evolution, Molecular; D016679:Genome, Viral; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017800:Potyvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D056910:Republic of Korea; D013025:Glycine max / Q000821:virology
keywords: Pathogenicity; Phylogenetic relationship; Population structure; Recombination; Soybean mosaic virus