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Best practices in metabarcoding of fungi: from experimental design to results
  • +5
  • Leho Tedersoo,
  • Mohammad Bahram,
  • Lucie Zinger,
  • Henrik Nilsson,
  • Peter Kennedy,
  • Teng Yang,
  • Sten Anslan,
  • Vladimir Mikryukov
Leho Tedersoo
University of Tartu

Corresponding Author:[email protected]

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Mohammad Bahram
University of Tartu
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Lucie Zinger
Institut de Biologie de l’ENS (IBENS), Département de Biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
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Henrik Nilsson
University of Gothenburg
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Peter Kennedy
University of Minnesota
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Teng Yang
Chinese Academy of Sciences
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Sten Anslan
Institution of Ecology and Earth Sciences
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Vladimir Mikryukov
Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences
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Abstract

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.
27 Sep 2021Submitted to Molecular Ecology
29 Sep 2021Submission Checks Completed
29 Sep 2021Assigned to Editor
15 Oct 2021Reviewer(s) Assigned
03 Dec 2021Review(s) Completed, Editorial Evaluation Pending
17 Dec 2021Editorial Decision: Revise Minor
07 Feb 2022Review(s) Completed, Editorial Evaluation Pending
07 Feb 20221st Revision Received
30 Mar 2022Editorial Decision: Accept
20 Apr 2022Published in Molecular Ecology. 10.1111/mec.16460