Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences

Seo, Jang‐Kyun; Ohshima, Kazusato; Lee, Hyeok-Geun; Son, Moonil; Choi, Hyun-Sug; Lee, Su-Heon; Sohn, Seong-Han; Kim, Kook‐Hyung

doi:10.1016/j.virol.2009.07.007

Cited by 124 publications

(100 citation statements)

References 56 publications

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“…This genomic region has also been recently detected as hotspot for recombination in several other members of potyvirus such as Sweet potato feathery mottle virus [22], Soybean mosaic virus (SMV) [23], and Watermelon mosaic virus [24]. Taken together with the previous studies [2,11,12,14,25], this study has also revealed that recombination is the major driving force in the emergence of new variants of SCMV.…”

supporting

confidence: 69%

Genomic evidence of intraspecific recombination in sugarcane mosaic virus

Padhi

Ramu²

2010

Virus Genes

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The sugarcane mosaic virus (SCMV) of the genus potyvirus, which primarily affects maize, sugarcane, sorghum, abaca, and grasses, occurs worldwide and causes significant economic loss. Using the full genome sequences of SCMV and several recombination detection methods, in this study we report that recombination is the major driving force in the evolution and emergence of several new variants of SCMV. We reported eight highly significant (P < 0.001) recombination break points, majority of which are located within 6K1-VPg-NIaPro-NIb region, thus indicating a region for recombination hotspot. The observation of commonalities of same recombination events among the SCMV isolates between the countries (Spain and Mexico), and within the country (within China, and within Mexico), suggests common origin of the isolates in respective regions.

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supporting

confidence: 69%

Genomic evidence of intraspecific recombination in sugarcane mosaic virus

Padhi

Ramu²

2010

Virus Genes

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“…Phylogenetic analysis did not indicate a clear relationship between genetic variability of BBrMV isolates and their geographical origin. Seo et al [19] reported that the phylogenetic trees were inconsistent and did not support geographic clustering of the Soybean mosaic virus (SMV) isolates. The phylogenetic inconsistency and clustering pattern in BBrMV isolates might be due to the movement of infected suckers across the districts of Tamil Nadu and other states in south India.…”

Section: Discussionmentioning

confidence: 99%

Population structure of Banana bract mosaic virus reveals recombination and negative selection in the helper component protease (HC-Pro) gene

et al. 2014

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Banana bract mosaic virus (BBrMV) is a serious constraint in the production of banana and plantain in India. In this study, we have cloned, sequenced and analyzed the helper component proteinase (HC-Pro) gene of 22 isolates from India and compared with previously reported BBrMV isolates. Sequence identity of BBrMV isolates encoding HC-Pro gene, were 92-100 % both at the nucleotide (nt) and amino acid level. Phylogenetic analysis based on nt sequences of non recombinant isolates showed that TN15, TN9 and TN24 formed one cluster and all the remaining isolates formed into another cluster. Different functional motifs in the central region of HC-Pro gene of BBrMV isolates were found conserved. Four potential recombinants with a total of 15 breakpoints were mostly observed at the N and a few from C terminal regions. The codon based selection analysis revealed that most of the codons were under purifying or negative selection except a codon at position 74 which was under positive selection. It is likely that recombination identified in Indian BBrMV isolates, along with strong purifying selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene. This study suggested that negative selection and recombination were important evolutionary factors driving the genetic diversification and population structure of Indian BBrMV isolates. To the best of our knowledge, this is the first report on the diversity analysis and occurrence of recombination in the HC-Pro gene of BBrMV.

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“…They have spread throughout much of the subtropical and temperate zones of the world King et al, 2012). Potato virus Y (Ogawa et al, 2008;Visser et al, 2012), turnip mosaic virus (TuMV) (Ohshima et al, 2002), soybean mosaic virus (Seo et al, 2009) and zucchini yellow mosaic virus (Lecoq et al, 2009) are important potyviruses with worldwide distributions. Nevertheless, there remains a poor understanding of how and when they dispersed, and of what factors controlled that spread.…”

Section: Introductionmentioning

confidence: 99%

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

Yasaka

Ohba

Schwinghamer

et al. 2015

Journal of General Virology

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Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter-and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three nonrecombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

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Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences

Cited by 124 publications

References 56 publications

Genomic evidence of intraspecific recombination in sugarcane mosaic virus

Genomic evidence of intraspecific recombination in sugarcane mosaic virus

Population structure of Banana bract mosaic virus reveals recombination and negative selection in the helper component protease (HC-Pro) gene

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand

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