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Its all fun guys: a comparison of bioinformatic pipelines for metabarcoding plant and soil fungal communities

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPAUVERT, Charlie
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorBUÉE, Marc
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorLAVAL, Valerie
hal.structure.identifierAgroécologie [Dijon]
dc.contributor.authorEDEL-HERMANN, Véronique
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorFAUCHERY, Laure
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorGAUTIER, Angelique
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierUnité Mixte de Recherche en Santé Végétale (INRA/ENITA) [UMRSV]
dc.contributor.authorVALLANCE, Jessica
ORCID: 0000-0002-5581-4453
IDREF: 143291556
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorVACHER, Corinne
dc.date.issued2018
dc.date.conference2018-12-04
dc.description.abstractEnFungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are classically studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic pipeline for the analysis of these data. We sequenced an artificial fungal community composed of 189 strains covering a wide range of Ascomycota and Basidiomycota, to compare the performance of 288 software and parameter combinations. The most sensitive pipelines, based on the USEARCH and VSEARCH clustering algorithms, detected almost all fungal strains but greatly overestimated the total number of strains. By contrast, pipelines using DADA2 to detect amplicon sequence variants were the most effective for recovering the richness and composition of the fungal community. Our results suggest that analyzing single forward (R1) sequences with DADA2 and no filter other than the removal of low-quality and chimeric sequences is a good option for fungal community characterization.
dc.language.isoen
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enBioinformatics
dc.subject.enEnvironmental DNA
dc.subject.enFungi
dc.subject.enIllumina MiSeq
dc.subject.enInternal transcribed spacer (ITS)
dc.subject.enMetabarcoding
dc.subject.enMock community
dc.subject.enDADA2
dc.subject.enUSEARCH
dc.subject.enVSEARCH
dc.title.enIts all fun guys: a comparison of bioinformatic pipelines for metabarcoding plant and soil fungal communities
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halSciences de l'environnement/Biodiversité et Ecologie
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
bordeaux.pagenp
bordeaux.countryFR
bordeaux.conference.cityMontpellier
bordeaux.peerReviewednon
hal.identifierhal-01938707
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2018-12-06
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01938707v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.date=2018&rft.spage=np&rft.epage=np&rft.au=PAUVERT,%20Charlie&BU%C3%89E,%20Marc&LAVAL,%20Valerie&EDEL-HERMANN,%20V%C3%A9ronique&FAUCHERY,%20Laure&rft.genre=conference


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