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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement and Virus Management of Small Fruit Crops

Location: Horticultural Crops Research

Title: De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs

item Sequin, J
item Rajeswaran, R
item Malpica, N
item Martin, Robert - Bob
item Kasschau, K
item Dolja, V
item Otten, P
item Farinelli, L
item Pooggin, M

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2014
Publication Date: 2/11/2014
Publication URL:
Citation: Sequin, J., Rajeswaran, R., Malpica, N., Martin, R.R., Kasschau, K., Dolja, V.V., Otten, P., Farinelli, L., Pooggin, M.M. 2014. De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from 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.

Last Modified: 07/25/2017
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