Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States

Cucumber mosaic virus (CMV) has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L.) in the Midwest and Northeastern United States. Virus diversity leading to emergence...

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Main Authors:	Nouri, Shahideh, Arevalo, Rafael, Falk, Bryce W., Groves, Russell L.
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012352/

id	pubmed-4012352
recordtype	oai_dc
spelling	pubmed-40123522014-05-09 Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States Nouri, Shahideh Arevalo, Rafael Falk, Bryce W. Groves, Russell L. Research Article Cucumber mosaic virus (CMV) has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L.) in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π) was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure. Public Library of Science 2014-05-06 /pmc/articles/PMC4012352/ /pubmed/24801880 http://dx.doi.org/10.1371/journal.pone.0096582 Text en © 2014 Nouri et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Nouri, Shahideh Arevalo, Rafael Falk, Bryce W. Groves, Russell L.
spellingShingle	Nouri, Shahideh Arevalo, Rafael Falk, Bryce W. Groves, Russell L. Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
author_facet	Nouri, Shahideh Arevalo, Rafael Falk, Bryce W. Groves, Russell L.
author_sort	Nouri, Shahideh
title	Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
title_short	Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
title_full	Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
title_fullStr	Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
title_full_unstemmed	Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States
title_sort	genetic structure and molecular variability of cucumber mosaic virus isolates in the united states
description	Cucumber mosaic virus (CMV) has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L.) in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π) was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012352/
_version_	1612086067229360128

Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States

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