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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Robert LückingBotanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, GermanyM. Catherine AimeDepartment of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USABarbara RobbertseNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USAAndrew N. MillerIllinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USAHiran A. AriyawansaDepartment of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, TaiwanTakayuki AokiInternational Commission on the Taxonomy of Fungi, Champaign, IL USAGianluigi CardinaliDepartment Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, ItalyP.W. CrousInternational Commission on the Taxonomy of Fungi, Champaign, IL USAIrina S. DruzhininaInternational Commission on the Taxonomy of Fungi, Champaign, IL USADavid M. GeiserDepartment of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USADavid L. HawksworthComparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UKKevin D. HydeCenter of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 ThailandLászló IrinyiMolecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW AustraliaRajesh JeewonDepartment of Health Sciences, Faculty of Science, University of Mauritius, Reduit, MauritiusPeter R. JohnstonInternational Commission on the Taxonomy of Fungi, Champaign, IL USAPaul M. KirkRoyal Botanic Gardens, Kew, Surrey, TW9 3DS UKElaine MalossoInternational Commission on the Taxonomy of Fungi, Champaign, IL USATom W. MayInternational Commission on the Taxonomy of Fungi, Champaign, IL USAWieland MeyerMolecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW AustraliaMaarja ÖpikUniversity of Tartu, 40 Lai Street, 51 005 Tartu, EstoniaVincent RobertDepartment Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, ItalyMarc StadlerDepartment Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, GermanyMarco ThinesInstitute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), GermanyDuong VuWesterdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The NetherlandsAndrey YurkovInternational Commission on the Taxonomy of Fungi, Champaign, IL USANing ZhangDepartment of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USAConrad L. SchochInternational Commission on the Taxonomy of Fungi, Champaign, IL USA

2020en

ABI

Annotatsiya

) 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.

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DOI: 10.1186/s43008-020-00033-z

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