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Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing

hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorLEGEAY, Jean
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
hal.structure.identifierMinistère de l'Agriculture de la Pêche et de l'Alimentation
dc.contributor.authorHUSSON, Claude
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorCORDIER, Tristan
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorVACHER, Corinne
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorMARÇAIS, Benoit
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorBUÉE, Marc
dc.date.issued2019
dc.identifier.issn1125-4653
dc.description.abstractEnOomycetes are eukaryotic plant pathogens that require health monitoring. High-throughput sequencing (HTS) methods replace progressively cultivation-based approaches in soil surveys of Oomycetes, but very little control has been done from synthetic communities. Indeed, several potential biases do exist and need to be assessed for Oomycetes communities. We created a mock community by mixing DNA from 24 Phytophthora species. We amplified two barcode regions with Oomycete-specific primers before HTS. With this aim, we used three primer sets in nested PCR amplification, targeting the ITS-1 region or the RAS gene region. The three nested PCR strategies proved to be a reliable qualitative approach, identifying approximately 95% of the species after Illumina Miseq sequencing and bioinformatic analysis. However, quantitative proportions of each species showed distortions compared to the original mixture of the mock. In addition, we compared the two ITS primer sets on soil environmental DNA sampled from temperate forests. The 'oom18S-ITS7/18ph2f-5.8S-1R' primer set, more specific to Phytophthora, was able to detect seven Phytophthora species, confirming what was expected for temperate forests. Using the 'DC6-ITS7/oom18S-ITS7' primer set that covers the broader Peronosporaceans, we detected only one Phytophthora species among the dominance of Pythium and Phytopythium species. We concluded that 'oom18S-ITS7/18ph2f-5.8S-1R' primer set is a reliable tool for the qualitative description of environmental Phytophthora communities.
dc.description.sponsorshipRecherches Avancées sur l'Arbre et les Ecosytèmes Forestiers - ANR-11-LABX-0002
dc.language.isoen
dc.publisherSpringer
dc.subject.enphytophthora
dc.subject.enmetabarcoding
dc.subject.enITS region
dc.subject.enRAS gene
dc.subject.enmock community
dc.subject.enPhytophthora
dc.subject.enMetabarcoding
dc.subject.enMock community
dc.title.enComparison and validation of Oomycetes metabarcoding primers for Phytophthora high throughput sequencing
dc.typeArticle de revue
dc.identifier.doi10.1007/s42161-019-00276-9
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalJournal of Plant Pathology
bordeaux.page743-748
bordeaux.volume101
bordeaux.issue3
bordeaux.peerReviewedoui
hal.identifierhal-02618173
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02618173v1
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