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Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata)

Pallett, Denise W.; Ho, Thien; Cooper, Ian; Wang, Hui. 2010 Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata). Journal of Virological Methods, 168. 223-227. 10.1016/j.jviromet.2010.06.003

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Abstract/Summary

Small RNA sequences were obtained from leaf extracts of wild Dactylis glomerata (cocksfoot grass) using deep sequencing (454 Life Sciences, Roche Diagnostics), and were screened against virus sequences in GenBank using a local BLASTn search program (BioEdit). Putative small interfering (si)RNAs complementary in sequence to Cereal yellow dwarf virus (CYDV, genus Luteovirus) genomes were identified. Primer sequences were made against the “high scoring” siRNA sequences and RT-PCR was used to amplify a 438 bp CYDV fragment in total RNA extracts from D. glomerata leaves. Sequencing of the RT-PCR product confirmed the occurrence of a previously undescribed CYDV population with phylogenetic affinity to CYDV-RPS. In D. glomerata the CYDV infection rates were 42.3% (n = 78) in 2008 and 50.0% (n = 48) in 2009. Specific RT-PCR tests also showed that this D. glomerata population harboured Cocksfoot streak virus (CSV, genus Potyvirus). Dual infections by these viruses were observed in 20.5–22.9% of all plants tested in 2008–2009. Interestingly, infections of either CYDV or CSV enhanced the occurrence of the other virus in individual grasses. Opportunities are discussed for using siRNA sequencing approaches in virus survey and other ecology studies under field conditions.

Item Type: Publication - Article
Digital Object Identifier (DOI): 10.1016/j.jviromet.2010.06.003
Programmes: CEH Topics & Objectives 2009 onwards > Biodiversity > BD Topic 1 - Observations, Patterns, and Predictions for Biodiversity
CEH Sections: CEH fellows
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ISSN: 0166-0934
Additional Keywords: virus detection, siRNA, high throughput sequencing, Cereal yellow dwarf virus, Cocksfoot streak virus, Dactylis glomerata
NORA Subject Terms: Biology and Microbiology
Date made live: 23 Sep 2010 13:10
URI: http://nora.nerc.ac.uk/id/eprint/10951

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