Decoding high-throughput sequencing data to address different layers of plant virus diversity
Denis Kutnjak: National Institute of Biology
<div>The unbiased nature and high data generation potential of high-throughput sequencing (HTS) technologies render them applicable to study viruses on multiple biological levels, from within the host to the ecosystem level. Starting within the host, HTS can be used to study the structures and dynamics of viral populations during virus evolution; using this approach, we characterized the structure of <em>Potato virus Y</em> (<em>Potyvirus</em>, <em>Potyviridae</em>) populations within plants and then tracked the changes in population structure of the virus during the experimental evolution in different host genotypes. We also applied HTS for detection of different viruses in plant samples and characterization of divergent viral strains (<em>Potato virus X</em>, <em>Potexvirus</em>, <em>Alphaflexiviridae</em>) and obscure viruses on new host plant species (<em>Henbane mosaic virus</em>, <em>Potyvirus</em>, <em>Potyviridae</em>). Finally, moving from single or few hosts to the ecosystem level, HTS can be employed for virome studies of environmental samples; water samples from a wastewater treatment plant were concentrated and subsequently we determined the viromes of those samples using HTS. A wide array of plant viruses was detected in these samples. Further infectivity assays using test plants confirmed the infectivity of some of the viruses detected using NGS approach. An overview illustrated with practical examples of the use of NGS across different levels of plant virus biodiversity will be discussed.</div>
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