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High-throughput sequencing (HTS) for detection and discovery of pineapple mealybug wilt associated viruses (PMWaV): comparison of five approaches

hal.structure.identifierUnité Ravageurs et agents pathogènes tropicaux [RAPT]
dc.contributor.authorMASSÉ, Delphine
hal.structure.identifierUnité Ravageurs et agents pathogènes tropicaux [RAPT]
dc.contributor.authorCASSAM, Nathalie
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorFERNANDEZ, Emmanuel
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorFILLOUX, Denis
hal.structure.identifierUnité Ravageurs et agents pathogènes tropicaux [RAPT]
dc.contributor.authorHOSTACHY, Bruno
hal.structure.identifierUnité de Pathologie Végétale [PV]
dc.contributor.authorVERDIN, Eric
hal.structure.identifierGembloux Agro-Bio Tech [Gembloux]
dc.contributor.authorMASSART, Sébastien
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMARAIS-COLOMBEL, Armelle
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorROUMAGNAC, Philippe
hal.structure.identifierPeuplements végétaux et bioagresseurs en milieu tropical [UMR PVBMT]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorLEFEUVRE, Pierre
hal.structure.identifierPeuplements végétaux et bioagresseurs en milieu tropical [UMR PVBMT]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorLETT, Jean-Michel
dc.date.conference2021-09-12
dc.description.abstractEnHTS technology are now routinely used for virus discovery, but have yet to replace more conventional approaches for virus detection. Here, we compared five different HTS methods for virus detection: 1) ribo-depleted total RNA, 2) Double-stranded RNA (dsRNA), 3) Virus-derived small interfering RNAs (siRNA), 4) Virion-associated nucleic acids (VANA), and 5) total RNA with Oxford Nanopore Technologies (ONT) and MinION plateform. Pineapples from Reunion Island, displaying wilt symptoms, were tested in order to properly assess the performance and application range of each method.From the combination of all generated sequences, we were able to assemble nearly full genomes of viruses known to be associated with the Mealybug wilt disease of pineapple: Four distinct Pineapple mealybug wilt-associated virus species (PMWaV1, -2, -3 and -5) and the Pineapple bacilliform comosus virus (PBCoV) were characterized. Moreover, the genomes of a Sadwavirus and three new viruses belonging to the Ampelovirus (n=2) and Vitivirus (n=1) genera were also fully assembled.The comparison of the detection of each virus, using each tested method proves that all were suitable for the detection of all viruses, providing a sufficient coverage depth. The results showed that the ribo-depleted total RNA appears to be the best strategy to obtain nearly complete genomes, whether for RNA or DNA viruses, with or without poly-A tail. Conversely, total RNA with ONT failed for the complete reconstruction of most viral genomes.Globally, the discovery of new viruses proves the importance of diagnostic HTS tests and their inclusivity in understanding disease etiology and further highlight the diversity of viruses associated with pineapple
dc.language.isoen
dc.subject.enpineapple mealybug wilt associated viruses (PMWaV)
dc.subject.enplant pathology
dc.subject.envirus
dc.title.enHigh-throughput sequencing (HTS) for detection and discovery of pineapple mealybug wilt associated viruses (PMWaV): comparison of five approaches
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie
bordeaux.conference.title18. Rencontres de virologie végétale (RVV 2021)
bordeaux.countryFR
bordeaux.conference.cityAussois
bordeaux.peerReviewednon
hal.identifierhal-03576172
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2021-09-16
hal.popularnon
hal.audienceNationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-03576172v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=MASS%C3%89,%20Delphine&CASSAM,%20Nathalie&FERNANDEZ,%20Emmanuel&FILLOUX,%20Denis&HOSTACHY,%20Bruno&rft.genre=unknown


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