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Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains

hal.structure.identifierSlovak Academy of Science [Bratislava] [SAS]
hal.structure.identifierSs. Cyril and Methodius University in Skopje [UKIM]
dc.contributor.authorGLASA, Miroslav
hal.structure.identifierSs. Cyril and Methodius University in Skopje [UKIM]
dc.contributor.authorHANČINSKÝ, Richard
hal.structure.identifierComenius University in Bratislava
dc.contributor.authorŠOLTYS, Katarína
hal.structure.identifierSlovak Academy of Science [Bratislava] [SAS]
dc.contributor.authorPREDAJŇA, Lukáš
hal.structure.identifierSlovak Academy of Science [Bratislava] [SAS]
hal.structure.identifierSs. Cyril and Methodius University in Skopje [UKIM]
dc.contributor.authorTOMAŠECHOVÁ, Jana
hal.structure.identifierNational Agriculture and Food Centre – Research Institute of Plant Production
dc.contributor.authorHAUPTVOGEL, Pavol
hal.structure.identifierSs. Cyril and Methodius University in Skopje [UKIM]
dc.contributor.authorMRKVOVÁ, Michaela
hal.structure.identifierSs. Cyril and Methodius University in Skopje [UKIM]
hal.structure.identifierNational Agriculture and Food Centre – Research Institute of Plant Production
dc.contributor.authorMIHÁLIK, Daniel
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
dc.date.issued2021
dc.identifier.issn2223-7747
dc.description.abstractEnIn 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
dc.language.isoen
dc.publisherMDPI
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectvirus phytopathogène
dc.subjectvirologie végétale
dc.subjectsanté des plantes
dc.subjectpathologie végétale
dc.subject.enGenome Mapping
dc.subject.ennext generation sequencing
dc.subject.enpotyvirus
dc.subject.enPVY
dc.subject.enSolanaceae
dc.title.enMolecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains
dc.typeArticle de revue
dc.identifier.doi10.3390/plants10040753
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalPlants
bordeaux.page753
bordeaux.volume10
bordeaux.issue4
bordeaux.peerReviewedoui
hal.identifierhal-03197142
hal.version1
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03197142v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Plants&rft.date=2021&rft.volume=10&rft.issue=4&rft.spage=753&rft.epage=753&rft.eissn=2223-7747&rft.issn=2223-7747&rft.au=GLASA,%20Miroslav&HAN%C4%8CINSK%C3%9D,%20Richard&%C5%A0OLTYS,%20Katar%C3%ADna&PREDAJ%C5%87A,%20Luk%C3%A1%C5%A1&TOMA%C5%A0ECHOV%C3%81,%20Jana&rft.genre=article


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