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A primer on the analysis of high-throughput sequencing data for detection of plant viruses

A primer on the analysis of high-throughput sequencing data for detection of plant viruses

Kutnjak, Denis, Tamisier, Lucie, Adams, Ian, Boonham, Neil, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Kreuze, Jan F., Lefebvre, Marie, Silva, Goncalo ORCID: 0000-0001-5544-2947, Malapi-Wight, Martha, Margaria, Paolo, Mavric Pleško, Irena, McGreig, Sam, Miozzi, Laura, Remenant, Benoit, Reynard, Jean-Sebastien, Rollin, Johan, Rott, Mike, Schumpp, Olivier, Massart, Sébastien and Haegeman, Annelies (2021) A primer on the analysis of high-throughput sequencing data for detection of plant viruses. Microorganisms, 9 (4):841. ISSN 2076-2607 (Online) (doi:https://doi.org/10.3390/microorganisms9040841)

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Abstract

High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.

Item Type: Article
Uncontrolled Keywords: plant virus; high-throughput sequencing; bioinformatics; detection; discovery
Subjects: S Agriculture > SB Plant culture
T Technology > TD Environmental technology. Sanitary engineering
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Molecular Virology and Entomology Research Group
Related URLs:
Last Modified: 30 Jul 2021 15:01
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
Selected for REF2021: None
URI: http://gala.gre.ac.uk/id/eprint/33414

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