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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)

By Denise W. Pallett, Thien Ho, Ian Cooper and Hui Wang

Abstract

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

Topics: Biology and Microbiology
Publisher: Elsevier
Year: 2010
DOI identifier: 10.1016/j.jviromet.2010.06.003
OAI identifier: oai:nora.nerc.ac.uk:10951
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