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Research article - Peer-reviewed, 2020

Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities

Castano, Carles; Berlin, Anna; Brandstrom Durling, Mikael; Ihrmark, Katharina; Lindahl, Bjorn D.; Stenlid, Jan; Clemmensen, Karina E.; Olson, Ake

Abstract

Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.

Keywords

high-throughput sequencing; Illumina MiSeq; ITS; metabarcoding; metabarcoding biases; mock community; PacBio

Published in

New Phytologist
2020, volume: 228, number: 3, pages: 1149-1158
Publisher: WILEY

Authors' information

Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Swedish University of Agricultural Sciences, Department of Soil and Environment
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology

UKÄ Subject classification

Microbiology
Genetics

Publication Identifiers

DOI: https://doi.org/10.1111/nph.16731

URI (permanent link to this page)

https://res.slu.se/id/publ/107178