Its all fun guys: a comparison of bioinformatic pipelines for metabarcoding plant and soil fungal communities
Language
en
Autre communication scientifique (congrès sans actes - poster - séminaire...)
This item was published in
2018-12-04, Montpellier. 2018p. np
English Abstract
Fungal 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 ...Read more >
Fungal 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.Read less <
English Keywords
Bioinformatics
Environmental DNA
Fungi
Illumina MiSeq
Internal transcribed spacer (ITS)
Metabarcoding
Mock community
DADA2
USEARCH
VSEARCH
Origin
Hal imported