Viruses Detection in a Wild Plant, Arctium tomentosum, by siRNA Deep-Sequencing

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http://urn.fi/URN:NBN:fi:hulib-201507211881
Title: Viruses Detection in a Wild Plant, Arctium tomentosum, by siRNA Deep-Sequencing
Author: Bi, Yaqi
Contributor: University of Helsinki, Faculty of Agriculture and Forestry, Department of Agricultural Sciences
Publisher: Helsingfors universitet
Date: 2012
Language: eng
URI: http://urn.fi/URN:NBN:fi:hulib-201507211881
http://hdl.handle.net/10138/29541
Thesis level: master's thesis
Discipline: Växtproduktions biologi (växtpatologi)
Plant Production Biology (Plant pathology)
Kasvintuotannon biologia (kasvipatologia)
Abstract: Plant is able to recognize dsRNA, and cleave the dsRNA into siRNA in the cell. This mechanism helps plant to against virus. A novel method of virus detection based on siRNA deep-sequencing has been developed. The method does not require any prior supposition, and it provides an unbiased view for detecting of all viruses. Thus it was used to detect viruses from a wild plant (Arctium tomentosum) with viral symptoms in Helsinki, Finland. Overlapping siRNA reads were used to build contigs using the program Velvet. Programs MAQ and Novoalign were used to align the siRNA reads to a reference sequence for the viral sequence recovery. In this study, two viruses, Alstroemeria virus X (AlsVX, genus Potexvirus, family Alphaflexiviridae) and Fig mosaic virus-Hel (FMV, unassigned genus Emaravirus) were identified. This is the first report for the occurrences of both viruses in Finland. The siRNA deep-sequencing detection results were confirmed by RT-PCR. The distributions of the viruses in Helsinki were also studied. Partial sequences of AlsVX-Hel and FMV-Hel were compared with related viruses in NCBI. The amino acid identity of the coat protein gene between AlsVX-Hel detected from Helsinki and AlsVX-Jap from Japan is 90%, and the amino acid identities of the putative nucleocapsid protein gene between FMV-Hel and other FMV strains were about 78%. The differences indicate that the AlsVX-Hel in Helsinki might be a new strain of AlsVX, and FMV-Hel might be a new strain of FMV, or a new virus.
Subject: wild plant
siRNA deep-sequencing
virus detection
Fig mosaic virus
Alstroemeria virus X
Arctium tomentosum


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