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High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

Author

Listed:
  • Miroslav Glasa

    (Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic)

  • Katarína Šoltys

    (Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovak Republic
    Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic)

  • Lukáš Predajňa

    (Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic)

  • Nina Sihelská

    (Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic)

  • Jaroslav Budiš

    (Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, Slovak Republic)

  • Michaela Mrkvová

    (Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovak Republic)

  • Ján Kraic

    (Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovak Republic
    National Agriculture and Food Centre, Research Institute of Plant Production, Piešťany, Slovak Republic)

  • Daniel Mihálik

    (Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovak Republic
    National Agriculture and Food Centre, Research Institute of Plant Production, Piešťany, Slovak Republic
    Institute of High Mountain Biology, University of Žilina, Žilina, Slovak Republic)

  • Ana Belén Ruiz-García

    (Instituto Valenciano de Investigaciones Agrarias, Center of Plant Protection and Biotechnology, Moncada, Spain)

Abstract

High-throughput sequencing (HTS) analysis of tomato (Solanum lycopersicum) samples revealed the presence of Potato virus M (PVM) in this crop in Slovakia. Full-length genomes of three PVM isolates were obtained using both HTS and Sanger sequencing validation. While two isolates (T40 and T50) were shown to belong to major Group I, a divergent T20 isolate was phylogenetically unrelated to any known PVM variant, potentially representing a new phylogenetic group. Despite a relatively high intraspecies diversity (17.3 ± 0.3%), no evidence of recombination was detected in the dataset of available complete PVM sequences. Conventional screening of tomato plants in Slovakia using ELISA and RT-PCR further confirmed a frequent occurrence of PVM in this host. Developed RT-PCR showed its polyvalence to detect the PVM Group I isolates, however, in silico analysis of primer binding sites indicated its compromised use for Group II isolates. Our results further pinpoint the significance of HTS for unbiased unveiling of virus diversity and a need for continual optimisation of molecular detection tools.

Suggested Citation

  • Miroslav Glasa & Katarína Šoltys & Lukáš Predajňa & Nina Sihelská & Jaroslav Budiš & Michaela Mrkvová & Ján Kraic & Daniel Mihálik & Ana Belén Ruiz-García, 2019. "High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus," Plant Protection Science, Czech Academy of Agricultural Sciences, vol. 55(3), pages 159-166.
    • Handle: RePEc:caa:jnlpps:v:55:y:2019:i:3:id:144-2018-pps
    DOI: 10.17221/144/2018-PPS
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