Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline
LAVAL, Valerie
BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
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BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
LAVAL, Valerie
BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
GAUTIER, Angelique
BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
< Reduce
BIOlogie et GEstion des Risques en agriculture [BIOGER]
Université Paris Saclay (COmUE)
Language
en
Article de revue
This item was published in
Fungal Ecology. 2019, vol. 41, p. 23 - 33
Elsevier
English Abstract
Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but ...Read more >
Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic approach 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 360 software and parameter combinations. The most sensitive approaches, based on the USEARCH and VSEARCH clustering algorithms, detected almost all fungal strains but greatly overestimated the total number of strains. By contrast, approaches 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. (C) 2019 Elsevier Ltd and British Mycological Society. All rights reserved.Read less <
Keywords
Bioinformatics
Environmental DNA
Illumina MiSeq
English Keywords
Fungi
Internal transcribed spacer (ITS)
Metabarcoding
Origin
Hal imported