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Replication data for: siRNA Deep Sequencing and Assembly: Piecing Together Viral Infections

International Potato Center Dataverse OAI Archive

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Title Replication data for: siRNA Deep Sequencing and Assembly: Piecing Together Viral Infections
 
Identifier https://doi.org/10.21223/P3/J0DRYE
 
Creator Kreuze, Jan
 
Publisher International Potato Center
 
Description RNA silencing constitutes a fundamental antiviral defense mechanism in plants in which host enzymes cut viral RNA into pieces of 20–24 nt. When isolated, sequenced en-mass and properly assembled or aligned these virus-derived small RNA (sRNA) sequences can reconstitute genomic sequence information of the viruses being targeted in the plant. This approach is independent of the ability to culture or purify the virus and does not require any specific amplification or enrichment of viral nucleic acids as it automatically enriches for small RNAs of viral origin by tapping into a natural antiviral defense mechanism. Using this technique known and novel DNA and RNA viruses as well as viroids have been identified at sensitivity levels comparable to PCR. This chapter will examine the strength and caveats of small RNA sequencing and assembly (sRSA), utilizing examples from literature as well as our own unpublished experiences and analysis of publically available plant sRNA sequence datasets.
 
Subject Agricultural Sciences
Diagnostics
Small-RNA
Sequencing
Assembly
Virus
Viroid
Detection
Plants
 
Language English
 
Contributor Administrator, CIP
CGIAR Research Program on Roots, Tubers and Bananas (RTB)
International Potato Center
De Paoli, Emanuele
Ruddat, Manfred
Fei, Zhangjun
 
Type fastq, doc, xls, txt