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De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs

Seguin, Jonathan and Rajeswaran, Rajendran and Malpica-López, Nachelli and Martin, Robert R. and Kasschau, Kristin and Dolja, Valerian V. and Otten, Patricia and Farinelli, Laurent and Pooggin, Mikhail M.. (2014) De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs. PLoS one, Vol. 9, H. 2 , e88513.

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Official URL: http://edoc.unibas.ch/dok/A6233649

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Abstract

Virus-infected plants accumulate abundant, 21-24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in both sense and antisense orientations. This implies pervasive transcription of both coding and non-coding viral DNA in the nucleus, which generates double-stranded RNA precursors of viral siRNAs. Consistent with our finding and hypothesis, we demonstrate that the complete genomes of DNA viruses from Caulimoviridae and Geminiviridae families can be reconstructed by deep sequencing and de novo assembly of viral siRNAs using bioinformatics tools. Furthermore, we prove that this 'siRNA omics' approach can be used for reliable identification of the consensus master genome and its microvariants in viral quasispecies. Finally, we utilized this approach to reconstruct an emerging DNA virus and two viroids associated with economically-important red blotch disease of grapevine, and to rapidly generate a biologically-active clone representing the wild type master genome of Oilseed rape mosaic virus. Our findings show that deep siRNA sequencing allows for de novo reconstruction of any DNA or RNA virus genome and its microvariants, making it suitable for universal characterization of evolving viral quasispecies as well as for studying the mechanisms of siRNA biogenesis and RNAi-based antiviral defense.
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Botanisches Institut > Pflanzenphysiologie Pathogenabwehr (Boller)
UniBasel Contributors:Pooggin, Mikhail and Malpica López, Hortensia Nachelli and Seguin, Jonathan
Item Type:Article, refereed
Bibsysno:Link to catalogue
Publisher:Public Library of Science
ISSN:1932-6203
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:05 Dec 2014 09:45
Deposited On:27 Mar 2014 13:13

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