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Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context

hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorFILLOUX, Denis
hal.structure.identifierComputational Biology Group, Institute of Infectious Diseases and Molecular Medicine
dc.contributor.authorMUHIRE, Brejnev
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
dc.contributor.authorJULLIAN, Charlotte
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorGALZI, Serge
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
dc.contributor.authorFORT, Guillaume
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
dc.contributor.authorBERNARDO, Pauline
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorDAUGROIS, Jean-Heindrich
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorFERNANDEZ, Emmanuel
hal.structure.identifierComputational Biology Group, Institute of Infectious Diseases and Molecular Medicine
dc.contributor.authorMARTIN, Darren P
hal.structure.identifierSchool of Biological Sciences and Biomolecular Interaction Centre
hal.structure.identifierDepartment of Plant Pathology and Emerging Pathogens Institute
hal.structure.identifierUniversity of Cape Town
dc.contributor.authorVARSANI, Arvind
hal.structure.identifierBiologie et Génétique des interactions Plantes-parasites pour la Protection Intégrée
hal.structure.identifierBiologie et Génétique des Interactions Plante-Parasite [UMR BGPI]
dc.contributor.authorROUMAGNAC, Philippe
dc.date.issued2014
dc.identifier.issn1932-6203
dc.description.abstractEnComprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations.
dc.language.isoen
dc.publisherPublic Library of Science
dc.title.enAppearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.pone.0102945
dc.subject.halSciences du Vivant [q-bio]/Sciences agricoles
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
bordeaux.journalPLoS ONE
bordeaux.volume9
bordeaux.issue7
bordeaux.peerReviewedoui
hal.identifierhal-02634210
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02634210v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS%20ONE&rft.date=2014&rft.volume=9&rft.issue=7&rft.eissn=1932-6203&rft.issn=1932-6203&rft.au=CANDRESSE,%20Thierry&FILLOUX,%20Denis&MUHIRE,%20Brejnev&JULLIAN,%20Charlotte&GALZI,%20Serge&rft.genre=article


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