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Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities

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Viral Metagenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1746))

Abstract

Viral metagenomic approaches have become essential for culture-independent and sequence-independent viral detection and characterization. This chapter describes an accurate and efficient approach to (1) concentrate viral particles from arthropods and plants, (2) remove contaminating non-encapsidated nucleic acids, (3) extract and amplify both viral DNA and RNA, and (4) analyze high-throughput sequencing (HTS) data by bioinformatics. Using this approach, up to 96 arthropod or plant samples can be multiplexed in a single HTS library.

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Acknowledgments

S.F. was supported by a scholarship from the National Institute of Agronomical Research (INRA) and from the University of Montpellier (UM). P.R. has received an EU grant FP7-PEOPLE-2013-IOF (N°PIOF-GA-2013-622571).

Author information

Authors and Affiliations

  1. NRA-UM, UMR DGIMI, Université de Montpellier F-34095, Montpellier, France

    Sarah François & Mylène Ogliastro

  2. CIRAD, UMR BGPI, Montpellier, France

    Denis Filloux, Emmanuel Fernandez & Philippe Roumagnac

  3. BGPI, CIRAD, NRA-UM, Montpellier SupAgro, Univ Montpellier, Montpellier, France

    Denis Filloux, Emmanuel Fernandez & Philippe Roumagnac

Authors
  1. Sarah François
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  2. Denis Filloux
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  3. Emmanuel Fernandez
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  4. Mylène Ogliastro
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  5. Philippe Roumagnac
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Corresponding author

Correspondence to Philippe Roumagnac .

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Editors and Affiliations

  1. Institute Sustainable Plant Protection of the CNR, Research Unit of Bari, Bari, Italy

    Vitantonio Pantaleo

  2. Institute Sustainable Plant Protection of the CNR, Research Unit of Bari, Bari, Italy

    Michela Chiumenti

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François, S., Filloux, D., Fernandez, E., Ogliastro, M., Roumagnac, P. (2018). Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities. In: Pantaleo, V., Chiumenti, M. (eds) Viral Metagenomics. Methods in Molecular Biology, vol 1746. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7683-6_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7683-6_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7682-9

  • Online ISBN: 978-1-4939-7683-6

  • eBook Packages: Springer Protocols

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