Plant Protect. Sci., 2019, 55(3):159-166 | DOI: 10.17221/144/2018-PPS

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

Miroslav Glasa*,1, Katarína Šoltys2,3, Lukáš Predajňa1, Nina Sihelská1, Jaroslav Budiš4, Michaela Mrkvová5, Ján Kraic5, 6, Daniel Mihálik5, 6, 7, Ana Belén Ruiz-García8
1 Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
2 Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovak Republic
3 Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
4 Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, Slovak Republic
5 Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovak Republic
6 National Agriculture and Food Centre, Research Institute of Plant Production, Piešťany, Slovak Republic
7 Institute of High Mountain Biology, University of Žilina, Žilina, Slovak Republic
8 Instituto Valenciano de Investigaciones Agrarias, Center of Plant Protection and Biotechnology, Moncada, Spain

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.

Keywords: PVM; Solanum lycopersicum L.; Carlavirus; full-length genome; RT-PCR; phylogenetical diversity

Published: September 30, 2019  Show citation

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Glasa M, Šoltys K, Predajňa L, Sihelská N, Budiš J, Mrkvová M, et al.. High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus. Plant Protect. Sci. 2019;55(3):159-166. doi: 10.17221/144/2018-PPS.
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