title: Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.
abstract: The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada.
authors.forename: Prasad
authors.initials: P
authors.lastname: Kesanakurti
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Belton
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada.
authors.forename: Hanaa
authors.initials: H
authors.lastname: Saeed
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada.
authors.forename: Heidi
authors.initials: H
authors.lastname: Rast
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada.
authors.forename: Ian
authors.initials: I
authors.lastname: Boyes
authors.affiliation: Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada. Electronic address: Mike.Rott@inspection.gc.ca.
authors.forename: Michael
authors.initials: M
authors.lastname: Rott
mesh_terms: D008403:Mass Screening / Q000379:methods* / Q000592:standards; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010942:Plant Viruses / Q000235:genetics / Q000302:isolation & purification*; D010944:Plants / Q000821:virology*; D012330:RNA, Double-Stranded / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012330:RNA, Double-Stranded; D012367:RNA, Viral
keywords: Black Turtle Soup; DsRNA; Next-generation sequencing; Plant quarantine; Plant viruses