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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #294530
Title: De novo reconstruction of plant RNA and DNA virus genomes from viral siRNAs

Author
item SEGUIN, JONATHAN - University Of Basel
item RAJENDRAN, RAJESWARAN - University Of Basel
item HORTENSIA, NACHELLI - University Of Basel
item Martin, Robert
item KASSCHAU, KRISTIN - Oregon State University
item DOLJA, VALERIAN - Oregon State University
item OTTEN, PATRICIA - Fasteris Sa
item FARINELLI, LAURENT - Fasteris Sa
item POOGGIN, MIKHAIL - University Of Basel

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2014
Publication Date: 2/11/2014
Citation: Seguin, J., Rajendran, R., Hortensia, N., Martin, R.R., Kasschau, K., Dolja, V., Otten, P., Farinelli, L., Pooggin, M. 2014. De novo reconstruction of plant RNA and DNA virus genomes from viral siRNAs. PLoS One. 9(2):e88513.

Interpretive Summary: Growing evidence indicates that 21-24 nucleotide viral small interfering RNAs are produced from double-stranded (ds)RNA precursors covering the entire viral genome sequences. Previous work has shown that this technology could be used to identify viruses that infect sweet potatoes. Here we report the application of the high throughput sequencing of small RNAs from plants to identify, viroids, RNA viruses and DNA viruses in a range of plant species. After initial studies on several known viruses in herbaceous hosts, the approach was used to examine grapevines that exhibited a red leaf symptom that was not associated with any known viruses. In this study, several viroids and a new DNA virus was detected in these symptomatic leaves. In adjacent symptomless grapevines only viroids were detected. This demonstrates that this technology can be used to identify unknown viruses in woody as well as herbaceous plants, opening up a new strategy to identify graft transmissible agents that cause a range of diseases in woody plants.

Technical Abstract: In antiviral defense, plants produce massive quantities of 21-24 nucleotide siRNAs. Here we demonstrate that the complete genomes of DNA and RNA viruses and viroids can be reconstructed by deep sequencing and de novo assembly of viral/viroid siRNAs from experimentally- and naturally-infected plants. We also show that bioinformatics analysis of viral siRNAs allows to identify cloning errors and reconstruct an infectious clone representing the master genome of viral quasispecies.