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

Miroslav Glasa, Katarína Šoltys, Lukáš Predajňa, Nina Sihelská, Jaroslav Budiš, Michaela Mrkvová, Ján Kraic, Daniel Mihálik and Ana Belén Ruiz-García
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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
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
Daniel Mihálik: Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Trnava, Slovak Republic
Ana Belén Ruiz-García: Instituto Valenciano de Investigaciones Agrarias, Center of Plant Protection and Biotechnology, Moncada, Spain

Plant Protection Science, 2019, vol. 55, issue 3, 159-166

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.

Keywords: PVM; Solanum lycopersicum L.; Carlavirus; full-length genome; RT-PCR; phylogenetical diversity (search for similar items in EconPapers)
Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlpps:v:55:y:2019:i:3:id:144-2018-pps

DOI: 10.17221/144/2018-PPS

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