Molecular characterisation of dicot-infecting mastreviruses from Australia

Hadfield, James; Thomas, J. E.; Schwinghamer, Mark W.; Kraberger, Simona; Stainton, Daisy; Dayaram, Anisha; Parry, J. N.; Pande, Daniel; Martin, Darren P.; Varsani, Arvind

doi:10.1016/j.virusres.2012.02.024

Cited by 41 publications

(26 citation statements)

References 42 publications

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“…Finally, unlike most organisms that have been studied, MSV exhibits high degrees of variance in CUB between different genes, and the reasons for this variation are unclear [33]. A single recently discovered eudicot-infecting mastrevirus sequence [65] exhibited codon usage preferences that differ from monocots, eudicots, and the other viruses we examined. Additional analysis is required to more precisely determine the forces affecting CUB in mastreviruses.…”

Section: Discussionmentioning

confidence: 99%

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Cardinale

DeRosa

Duffy

2013

Viruses

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Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.

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Section: Discussionmentioning

confidence: 99%

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Cardinale

DeRosa

Duffy

2013

Viruses

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“…Mastreviruses (type species Maize streak virus , MSV) are transmitted by leafhoppers (order Hemiptera, family Cicadellidae) and have a single genome component. Except for a recent identification of mastreviruses in sweet potato in Peru (Kreuze et al ., ) and in dragonflies (suborder Anisoptera) in Puerto Rico (Rosario et al ., ), these viruses have been found only in the Old World, where they infect a range of monocotyledonous plants (reviewed in Brown et al ., ) and, from recent reports, dicotyledonous plants (Hadfield et al ., ; Liu et al ., ; Nahid et al ., ). Mastreviruses have four ORFs, V1 and V2 on the virion‐sense strand, and C1 and C2 on the complementary‐sense strand, separated by two IRs on opposite sides of the genome, designated as large (LIR) and small (SIR) (Kammann et al ., ) (Fig.…”

Section: Introductionmentioning

confidence: 99%

Geminivirus protein structure and function

Fondong

2013

Molecular Plant Pathology

229

137

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Geminiviruses are a family of plant viruses that cause economically important plant diseases worldwide. These viruses have circular single-stranded DNA genomes and four to eight genes that are expressed from both strands of the double-stranded DNA replicative intermediate. The transcription of these genes occurs under the control of two bidirectional promoters and one monodirectional promoter. The viral proteins function to facilitate virus replication, virus movement, the assembly of virus-specific nucleoprotein particles, vector transmission and to counteract plant host defence responses. Recent research findings have provided new insights into the structure and function of these proteins and have identified numerous host interacting partners. Most of the viral proteins have been shown to be multifunctional, participating in multiple events during the infection cycle and have, indeed, evolved coordinated interactions with host proteins to ensure a successful infection. Here, an up-to-date review of viral protein structure and function is presented, and some areas requiring further research are identified.

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“…As it has been mentioned previously with different genomic data collected through studies of CSD recombination has played a key role in evolution of dicot infecting Masterviruses [13,30]. The infection of CpCDV to squash First genome analysis and molecular characterization 39 plants could be explained by the enormous pressure that can be faced in Mansoria region in Egypt where the squash field crop is planted in several areas as a unique cash crop very near to faba bean in several planting rounds puts a huge force to the vectors to transfer to another host plant and adapt to these hosts.…”

Section: Discussionmentioning

confidence: 84%

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

2015

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This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.

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Molecular characterisation of dicot-infecting mastreviruses from Australia

Cited by 41 publications

References 42 publications

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Base Composition and Translational Selection are Insufficient to Explain Codon Usage Bias in Plant Viruses

Geminivirus protein structure and function

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

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