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

Abstract

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.

Identification of viruses infecting cucurbits and determination of genetic diversity of Cucumber mosaic virus in Lorestan province, Iran

“…Th e virus diversity cannot be attributed to the eff ects of hosting as has been demonstrated in previous research from USA and China (Liu et al 2009;Nouri et al 2014). Our results also showed that host diff erences cannot be attributed to the genetic diversity.…”

“…Negative selection can reduce genetic variation in a population of viruses and increase the maintenance of coat protein stability. Negative selection of CMV coat protein abundance has been reported in previous studies (Liu et al 2009;Nouri et al 2014).…”

Çanakkale ili börülce üretim alanlarında Hıyar mozaik virüsü (Cucumber mosaic virus; CMV)’nün tespiti ve kılıf protein genine göre moleküler karakterizasyonu

“…Ülkemizde biber, domates ve kavun bitkilerinde CMV enfeksiyonunun karakterizasyonu amacı ile gerçekleştirilen bir çalışmada CMV izolatlarının alt grup IA'ya ait olduğu bulunmuştur (Çağlar 2006). Her iki çalışmada Türkiye'de gerçekleştirilmesine rağmen, aynı bölge izolatlarının farklı alt gruplarda olabileceği bilinmektedir (Nouri et al 2014, Eyvazi et al 2015, Ohshima et al 2016. Salem et al (2010) Gerçekleştirilen bu çalışma ile Türkiye'de ilk kez CMV enfeksiyonu ticari olarak börülce yetiştiriciliği yapılan alanlarda doğal enfeksiyon olarak tespit edilmiştir.…”

Estandarización de un método de detección molecular del Cucumber mosaic virus (cmv) en banano ecuatoriano

“…Las secuencias disponibles reportadas en GenBank para cmv aislado en banano americano tienen los siguientes números de accesión: AM055602.1, DQ640743.1, AM158321.1, DQ152254.1, U32858.1, U32859.1, M98501.1, M57602.1. Para alinear las secuencias se utilizó el programa BioEdit® (versión 5.0.9.1) y se buscaron secuencias de consenso de 18 a 25 pb (Nouri et al 2014). Para el diseño de cebadores se utilizó el programa Primer3 (versión 0.4.0) y se configuraron parámetros para descartar primers con alta formación de dímeros o con hibridaciones inespecíficas (Medrano et al 2006).…”

“…El ARN 1 y el ARN 2 codifican proteínas que intervienen en la replicación, además de codificar proteínas multifuncionales. El ARN 3 codifica las proteínas de la cápside y del movimiento (Nouri et al 2014). Los ARN subgenómicos (RNA 4 y RNA 4A) codifican para la CP (proteína de la cápside) y para la 2b (proteína supresora del silenciamiento génico) (Ding et al 1994;Jacquemond 2012).…”