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Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorSCHÖNEGGER, Deborah
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorMOUBSET, Oumaima
hal.structure.identifierLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
dc.contributor.authorMARGARIA, Paolo
hal.structure.identifierLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
dc.contributor.authorMENZEL, Wulf
hal.structure.identifierLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
dc.contributor.authorWINTER, Stephan
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
hal.structure.identifierDépartement Systèmes Biologiques [Cirad-BIOS]
dc.contributor.authorROUMAGNAC, Philippe
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMARAIS, Armelle
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
dc.date.accessioned2024-04-11T10:06:32Z
dc.date.available2024-04-11T10:06:32Z
dc.date.issued2023-11-30
dc.identifier.issn0022-538X
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197553
dc.description.abstractEnIn contrast to microbial metagenomics, there has still been only limited efforts to benchmark performance of virome analysis approaches in terms of faithfulness to community structure and of completeness of virome description. While natural communities are more readily accessible, synthetic communities assembled using well-characterized isolates allow more accurate performance evaluation. Starting from authenticated, quality-controlled reference isolates from the DSMZ Plant Virus Collection, we have assembled synthetic communities of varying complexity up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 viral families and 61 genera. These communities were then analyzed using two approaches frequently used in ecology-oriented plant virus metagenomics: a virion-associated nucleic acids (VANA)-based strategy and a highly purified double-stranded RNAs (dsRNAs)-based one. The results obtained allowed to compare diagnostic sensitivity of these two approaches for groups of viruses and satellites with different genome types and confirmed that the dsRNA-based approach provides a more complete representation of the RNA virome. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choiceif analysis of DNA viruses is of importance. They also allowed to identify several important parameters and to propose hypotheses to explain differences in performance, in particular, differences in the imbalance in the representation of individual viruses using each approach. Remarkably, these analyses highlight a strong direct relationship between the completeness of virome description and sample sequencing depth which should prove useful in further virome analysis efforts. IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
dc.description.sponsorshipMesure et cartographie de la richesse des virus des plante à l'échelle de l'écosytème - ANR-19-CE35-0008
dc.language.isoen
dc.publisherAmerican Society for Microbiology
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.envirome
dc.subject.enVANA
dc.subject.endsRNA
dc.subject.ensynthetic community
dc.subject.enmetagenome
dc.subject.endouble-stranded36 RNA
dc.subject.enhigh-throughput sequencing
dc.title.enBenchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community
dc.typeArticle de revue
dc.identifier.doi10.1128/jvi.01300-23
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalJournal of Virology
bordeaux.pagee0130023
bordeaux.volume97
bordeaux.hal.laboratoriesBiologie du Fruit & Pathologie (BFP) - UMR 1332*
bordeaux.issue11
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-04384795
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04384795v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Journal%20of%20Virology&rft.date=2023-11-30&rft.volume=97&rft.issue=11&rft.spage=e0130023&rft.epage=e0130023&rft.eissn=0022-538X&rft.issn=0022-538X&rft.au=SCH%C3%96NEGGER,%20Deborah&MOUBSET,%20Oumaima&MARGARIA,%20Paolo&MENZEL,%20Wulf&WINTER,%20Stephan&rft.genre=article


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