IMA Fungus 11(1): e33884, doi: 10.1186/s43008-020-00033-z
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
Robert Lücking‡, M. Catherine Aime§, Barbara Robbertse|, Andrew N. Miller¶, Hiran A. Ariyawansa¶, Takayuki Aoki, Gianluigi Cardinali#, Pedro W. Crous¤, Irina S. Druzhinina¶, David M. Geiser«, David L. Hawksworth», Kevin D. Hyde˄, Laszlo Irinyi˅, Rajesh Jeewon¦, Peter R. Johnstonˀ, Paul M. Kirkˁ, Elaine Malosso¶, Tom W. May, Wieland Meyer₵, Maarja Öpik¶, Vincent Robert, Marc Stadlerℓ, Marco Thines₰, Duong Vu, Andrey M. Yurkov¶, Ning Zhang₱, Conrad L. Schoch₳‡ Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany§ Purdue University, Department of Botany & Plant Pathology, West Lafayette| National Institutes of Health, Center for Biotechnology Information, National Library of Medicine, Bethesda¶ International Commission on the Taxonomy of Fungi, Champaign# University of Perugia, Department Pharmaceutical Sciences, Perugia, Italy¤ CBS-KNAW Fungal Biodiversity Centre, Utrecht« The Pennsylvania State University, Department of Plant Pathology & Environmental Microbiology, University Park» Universidad Complutense de Madrid, Departamento de Biología Vegetal II, Facultad de Farmacia, Madrid, Spain˄ Mae Fah Luang University, Center of Excellence in Fungal Research, Chiang Rai, Thailand˅ The University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Sydney, Australia¦ University of Mauritius, Department of Health Sciences, Faculty of Science, Reduit, Mauritiusˀ Manaaki Whenua Landcare Research, Auckland, New Zealandˁ CABI - Europe, Bakeham Lane, Egham, Surrey₵ University of Sydney Centre for Infectious Diseases and Microbiology, ICPMR, Level 3, Molecular Mycology Research Laboratory, Westmead Millennium Institute, Sydney Medical School - Westmead, Westmead, Australiaℓ Helmholtz Centre for Infection Research, Department Microbial Drugs, Brunswick, Germany₰ Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany₱ Rutgers University, Department of Plant Biology, New Brunswick₳ National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine, Bethesda
© Robert Lücking, M. Aime, Barbara Robbertse, Andrew Miller, Hiran Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro Crous, Irina Druzhinina, David Geiser, David Hawksworth, Kevin Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter Johnston, Paul Kirk, Elaine Malosso, Tom May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey Yurkov, Ning Zhang, Conrad Schoch. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY-NC 4.0), which permits to copy and distribute the article for non-commercial purposes, provided that the article is not altered or modified and the original author and source are credited. Citation:
Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11(1): e33884. https://doi.org/10.1186/s43008-020-00033-z |  |
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
Keywords
COX1, COX2, Oxford Nanopore technologies, PacBio, RPB2, Read placement, Species concepts, TEF1