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Virus Res. 2015 Oct 2;208:189-98. doi: 10.1016/j.virusres.2015.06.011. Epub 2015 Jun 21.

The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates.

Author information

1
Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China.
2
National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing 210095, China.
3
College of Resources and Environment, Northeast Agriculture University, Harbin 150030, China.
4
College of Agriculture, Northeast Agriculture University, Harbin 150030, China.
5
Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China. Electronic address: binwang@nju.edu.cn.
6
Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, Nanjing 210023, China. Electronic address: chenjq@nju.edu.cn.

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.

KEYWORDS:

Pathogenicity; Phylogenetic relationship; Population structure; Recombination; Soybean mosaic virus

PMID:
26103098
DOI:
10.1016/j.virusres.2015.06.011
[Indexed for MEDLINE]

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