Partial Sequence and Survey Analysis Identify a Multipartite, Negative-Sense RNA Virus Associated with Fig Mosaic

Walia, Jeewan Jyot; Salem, Nidà; Falk, Bryce W.

doi:10.1094/pdis-93-1-0004

Cited by 47 publications

(40 citation statements)

References 19 publications

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“…Although emaravirus genomes are multipartite in nature, individual members differ substantially in the number of genomic RNAs they possess. European mountain ash ringspot-associated virus (EMARaV), the type species of the Emaravirus genus (2,3), and Rose rosette virus (RRV) (4) are quadripartite; Pigeonpea sterility mosaic virus (PPSMV) (5,6) and Raspberry leaf blotch virus (RLBV) (7) are pentapartite; and Fig mosaic virus (FMV) (8)(9)(10)) is a hexapartite virus. The diverse number of genomic RNA segments suggests that emaraviruses evolve by acquiring additional genomic RNAs in order to facilitate precise virus-host and virus-vector interactions for virus survival.…”

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confidence: 99%

An Eriophyid Mite-Transmitted Plant Virus Contains Eight Genomic RNA Segments with Unusual Heterogeneity in the Nucleocapsid Protein

Satyanarayana

McMechan

Wosula

et al. 2014

J Virol

108

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Eriophyid mite-transmitted, multipartite, negative-sense RNA plant viruses with membrane-bound spherical virions are classified in the genus Emaravirus. We report here that the eriophyid mite-transmitted Wheat mosaic virus (WMoV), an Emaravirus, contains eight genomic RNA segments, the most in a known negative-sense RNA plant virus. Remarkably, two RNA 3 consensus sequences, encoding the nucleocapsid protein, were found with 12.5% sequence divergence, while no heterogeneity was observed in the consensus sequences of additional genomic RNA segments. The RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid, and P4 proteins of WMoV exhibited limited sequence homology with the orthologous proteins of other emaraviruses, while proteins encoded by additional genomic RNA segments displayed no significant homology with proteins reported in GenBank, suggesting that the genus Emaravirus evolved further with a divergent octapartite genome. Phylogenetic analyses revealed that WMoV formed an evolutionary link between members of the Emaravirus genus and the family Bunyaviridae. Furthermore, genomic-length virus-and virus-complementary (vc)-sense strands of all WMoV genomic RNAs accumulated asymmetrically in infected wheat, with 10-to 20-fold more virus-sense genomic RNAs than vc-sense RNAs. These data further confirm the octapartite negative-sense polarity of the WMoV genome. In WMoV-infected wheat, subgenomic-length mRNAs of vc sense were detected for genomic RNAs 3, 4, 7, and 8 but not for other RNA species, suggesting that the open reading frames present in the complementary sense of genomic RNAs are expressed through subgenomic-or near-genomic-length vc-sense mRNAs. IMPORTANCEWheat mosaic virus (WMoV), an Emaravirus, is the causal agent of High Plains disease of wheat and maize. In this study, we demonstrated that the genome of WMoV comprises eight negative-sense RNA segments with an unusual sequence polymorphism in an RNA encoding the nucleocapsid protein but not in the additional genomic RNA segments. WMoV proteins displayed weak or no homology with reported emaraviruses, suggesting that the genus Emaravirus further evolved with a divergent octapartite genome. The current study also examined the profile of WMoV RNA accumulation in wheat and provided evidence for the synthesis of subgenomic-length mRNAs of virus complementary sense. This is the first report to demonstrate that emaraviruses produce subgenomic-length mRNAs that are most likely utilized for genome expression. Importantly, this study facilitates the examination of gene functions and virus diversity and the development of effective diagnostic methods and management strategies for an economically important but poorly understood virus. E riophyid mite-transmitted, multipartite single-stranded RNA plant viruses with negative polarity recently were classified in the genus Emaravirus (1). The Emaravirus virions are membranebound particles of 80 to 200 nm in diameter, resembling those of Tospovirus. Members of the genus Emaravirus possess four...

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An Eriophyid Mite-Transmitted Plant Virus Contains Eight Genomic RNA Segments with Unusual Heterogeneity in the Nucleocapsid Protein

Satyanarayana

McMechan

Wosula

et al. 2014

J Virol

108

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“…Each anti-genomic segment is monocistronic. RNA 1 encodes for an RdRp, RNA 2 encodes a putative glycoprotein precursor, RNA 3 encodes a nucleocapsid (NP) protein, RNA 4 encodes a putative movement protein, and RNA 5 and RNA 6 encode proteins of unknown functions (13,24,25,52). The genome organization and the deduced amino acid sequences of FMV-encoded proteins are similar to those of another eriophyid mite-transmitted virus, European mountain ash ringspot associated virus (EMARAV).…”

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confidence: 99%

“…The genome organization and the deduced amino acid sequences of FMV-encoded proteins are similar to those of another eriophyid mite-transmitted virus, European mountain ash ringspot associated virus (EMARAV). Based on this, the genus Emaravirus (unassigned family) was proposed which contains EMARAV and tentatively three other species, one of which is FMV (12,24,38,52).In this study, we estimated the genetic variation and population structure of FMV isolates collected from diverse worldwide locations by analyzing the nucleotide sequences of four regions, one each of genomic RNAs 1, 2, 3, and 4. The roles of the evolutionary factors recombination, selection, genetic drift, and gene flow were examined.…”

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Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

Walia¹,

Willemsen²,

Elçi³

et al. 2014

Phytopathology®

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In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses.Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.RNA virus populations, including those within an individual virus-infected host or those in different host individuals, are heterogeneous in nature. For RNA viruses, this is often attributed to their large population sizes, short generation times, and high mutation rates from error-prone replication by the viral RNAdependent RNA polymerase (RdRp), which lacks a proofreading activity (9). Additional sources which can give rise to genetic variation include genome recombination and reassortment (39). The genetic diversity and structure of virus populations are limited and shaped by natural selection, genetic drift, and gene flow (37). The effects of these evolutionary mechanisms are also affected by the virus biology (e.g., host type and range, and means and extent of spread), the ecological environment, and population parameters (e.g., population size and history of population bottlenecks). Understanding the factors involved in the genetic diversity and structure of virus populations is fundamental for designing effective strategies for disease control or virus eradication (1).Like many animal viruses and bacteriophages, some RNA plant viruses have measurably evolving populations (11,20) whereas others evolve more slowly and have genetically stable populations (19). Two key aspects affecting virus evolution are the means of spread and host type. Plant viruses mostly utilize specific vectors for their plant-to-plant transmission (40). Plant-to-plant spread of viruses among herbaceous annual plants may be rapid and the life of the plant host is relatively short. Thus, these viruses are constantly infecting and adapting to new plant hosts. By contrast, the chronic infections in woody perennial plants can last for decades, with or without observable symptoms (44). In addition, most perennial crop plants are vegetatively propagated. If source plants used for propagation are virus infected, this provides opportunity for efficient transfer and mainten...

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“…Only recently the causal agent of FMD, a multipartite single-stranded negative-sense RNA virus belonging to the genus Emaravirus, was identified. Although Koch's postulates remain to be fulfilled due to the difficulty of sap inoculation (Elbeaino et al, 2009a), the strong association of FMV with FMD (Walia et al, 2009) and mite transmissibility of FMV (Çaglayan et al, 2010) Walia et al, 2009;Çağlayan et al, 2010;Ishikawa et al, 2012, Elbeshey andCaglar et al, 2011;El Air et al, 2015;Aldhebiani et al, 2015;Shahmirzaie et al, 2010).…”

Section: Fig Main Pests and Diseasesmentioning

confidence: 99%

Use of standard and setup of non conventional techniques for the elimination of viruses associated with Fig Mosaic Disease (FMD) in fig germplasm (Ficus carica L.)

Yahyaoui¹

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Partial Sequence and Survey Analysis Identify a Multipartite, Negative-Sense RNA Virus Associated with Fig Mosaic

Cited by 47 publications

References 19 publications

An Eriophyid Mite-Transmitted Plant Virus Contains Eight Genomic RNA Segments with Unusual Heterogeneity in the Nucleocapsid Protein

An Eriophyid Mite-Transmitted Plant Virus Contains Eight Genomic RNA Segments with Unusual Heterogeneity in the Nucleocapsid Protein

Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

Use of standard and setup of non conventional techniques for the elimination of viruses associated with Fig Mosaic Disease (FMD) in fig germplasm (Ficus carica L.)

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