Journal article
Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs
Virus research, Vol.178(2), pp.306-313
12/26/2013
Handle:
https://hdl.handle.net/2376/106383
PMID: 24076299
Abstract
•Rubus yellow net virus (RYNV) complete genomic sequence.•Sequences indicate RYNV is a distantly related member of the genus Badnavirus.•A full length clone confirmed validity of the genomic sequence.•Detected virus-derived small RNA (vsRNA) in RYNV infected raspberry tissue.•Mapping vsRNA showed uneven genome-wide clustering in both RYNV strands.
Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants.
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Details
- Title
- Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs
- Creators
- Melanie L Kalischuk - Department of Plant Pathology, Washington State University, Pullman, WA 99164-106, United StatesAdriana F Fusaro - School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, AustraliaPeter M Waterhouse - School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, AustraliaHanu R Pappu - Department of Plant Pathology, Washington State University, Pullman, WA 99164-106, United StatesLawrence M Kawchuk - Agriculture and Agri-Food Canada, P.O. Box 3000, Lethbridge, Alberta T1J 4B1, Canada
- Publication Details
- Virus research, Vol.178(2), pp.306-313
- Academic Unit
- Plant Pathology, Department of
- Publisher
- Elsevier B.V
- Identifiers
- 99900547069301842
- Language
- English
- Resource Type
- Journal article