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siRNA Deep Sequencing and Assembly: Piecing Together Viral Infections

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Detection and Diagnostics of Plant Pathogens

Part of the book series: Plant Pathology in the 21st Century ((ICPP,volume 5))

Abstract

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strength and caveats of small RNA sequencing and assembly (sRSA), utilizing examples from literature as well as our own unpublished experiences and analysis of publically available plant sRNA sequence datasets.

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Acknowledgments

I acknowledge the contributions from the various present and previous members of my lab and colleagues at CIP, and Emanuele De Paoli and Manfred Ruddat for sharing information about the samples from their small RNA libraries. Sincere thanks also to Zhangjun Fei for critical reading and useful comments of this chapter. The work on sRSA in our lab has been funded by grants from the Howard Buffet Foundation (subgrant 20127-C), Bill and Melinda Gates Foundation through the SASHA project (Grant OPP53344), the National Science Foundation through its BREAD program (Award No. 1110080), ICGEB-TWAS-UNESCO/IBSP Joint Programme on Capacity Building in Basic Molecular Biology (Contract No.: CRP/101005) and EU FP7 through the QBOL project (Grant No. 226482).

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Authors and Affiliations

  1. Laboratory of Virology, Peru International Potato Center (CIP), Avenida la Molina, 1895, La Molina, Peru

    Jan Kreuze

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  1. Jan Kreuze
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Correspondence to Jan Kreuze .

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Editors and Affiliations

  1. AGROINNOVA, University of Torino, Grugliasco, Torino, Italy

    Maria Lodovica Gullino

  2. Plant Research International, Wageningen UR, Wageningen, Utrecht, The Netherlands

    Peter J. M. Bonants

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Kreuze, J. (2014). siRNA Deep Sequencing and Assembly: Piecing Together Viral Infections. In: Gullino, M., Bonants, P. (eds) Detection and Diagnostics of Plant Pathogens. Plant Pathology in the 21st Century, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9020-8_2

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