Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains
In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples f...
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doaj-8e3981688d5841c1b3501f32b64e12312021-04-12T23:05:00ZengMDPI AGPlants2223-77472021-04-011075375310.3390/plants10040753Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY StrainsMiroslav Glasa0Richard Hančinský1Katarína Šoltys2Lukáš Predajňa3Jana Tomašechová4Pavol Hauptvogel5Michaela Mrkvová6Daniel Mihálik7Thierry Candresse8Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, SlovakiaComenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, 84104 Bratislava, SlovakiaBiomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, SlovakiaBiomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, SlovakiaNational Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešťany, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, SlovakiaFaculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, SlovakiaINRAE, Univ. Bordeaux, UMR BFP, 33140 Villenave d’Ornon, FranceIn recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.https://www.mdpi.com/2223-7747/10/4/753genomenext generation sequencingpotyvirusPVYSolanaceae |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Miroslav Glasa Richard Hančinský Katarína Šoltys Lukáš Predajňa Jana Tomašechová Pavol Hauptvogel Michaela Mrkvová Daniel Mihálik Thierry Candresse |
spellingShingle |
Miroslav Glasa Richard Hančinský Katarína Šoltys Lukáš Predajňa Jana Tomašechová Pavol Hauptvogel Michaela Mrkvová Daniel Mihálik Thierry Candresse Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains Plants genome next generation sequencing potyvirus PVY Solanaceae |
author_facet |
Miroslav Glasa Richard Hančinský Katarína Šoltys Lukáš Predajňa Jana Tomašechová Pavol Hauptvogel Michaela Mrkvová Daniel Mihálik Thierry Candresse |
author_sort |
Miroslav Glasa |
title |
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains |
title_short |
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains |
title_full |
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains |
title_fullStr |
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains |
title_full_unstemmed |
Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains |
title_sort |
molecular characterization of potato virus y (pvy) using high-throughput sequencing: constraints on full genome reconstructions imposed by mixed infection involving recombinant pvy strains |
publisher |
MDPI AG |
series |
Plants |
issn |
2223-7747 |
publishDate |
2021-04-01 |
description |
In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection. |
topic |
genome next generation sequencing potyvirus PVY Solanaceae |
url |
https://www.mdpi.com/2223-7747/10/4/753 |
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