Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?
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 e...
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2020-07-01
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| Series: | IMA Fungus |
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| Online Access: | http://link.springer.com/article/10.1186/s43008-020-00033-z |
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| author | 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. Johnston Paul M. Kirk Elaine Malosso Tom W. May Wieland Meyer Maarja Öpik Vincent Robert Marc Stadler Marco Thines Duong Vu Andrey M. Yurkov Ning Zhang Conrad L. Schoch |
| author_facet | 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. Johnston Paul M. Kirk Elaine Malosso Tom W. May Wieland Meyer Maarja Öpik Vincent Robert Marc Stadler Marco Thines Duong Vu Andrey M. Yurkov Ning Zhang Conrad L. Schoch |
| author_sort | Robert Lücking |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-976162c8e22842139067716b573524e9 |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2020-07-01 |
| publisher | BMC |
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| series | IMA Fungus |
| spelling | doaj-art-976162c8e22842139067716b573524e92025-02-02T20:07:07ZengBMCIMA Fungus2210-63592020-07-0111113210.1186/s43008-020-00033-zUnambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?Robert Lücking0M. Catherine Aime1Barbara Robbertse2Andrew N. Miller3Hiran A. Ariyawansa4Takayuki Aoki5Gianluigi Cardinali6Pedro W. Crous7Irina S. Druzhinina8David M. Geiser9David L. Hawksworth10Kevin D. Hyde11Laszlo Irinyi12Rajesh Jeewon13Peter R. Johnston14Paul M. Kirk15Elaine Malosso16Tom W. May17Wieland Meyer18Maarja Öpik19Vincent Robert20Marc Stadler21Marco Thines22Duong Vu23Andrey M. Yurkov24Ning Zhang25Conrad L. Schoch26Botanischer Garten und Botanisches Museum, Freie Universität BerlinInternational Commission on the Taxonomy of FungiNational Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiDepartment Pharmaceutical Sciences, University of PerugiaInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiDepartment of Plant Pathology & Environmental Microbiology, The Pennsylvania State UniversityInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiMolecular 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 ResearchDepartment of Health Sciences, Faculty of Science, University of MauritiusInternational Commission on the Taxonomy of FungiRoyal Botanic Gardens, KewInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiMolecular 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 ResearchInternational Commission on the Taxonomy of FungiDepartment Pharmaceutical Sciences, University of PerugiaInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiWesterdijk Fungal Biodiversity InstituteInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiInternational Commission on the Taxonomy of FungiABSTRACT 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.http://link.springer.com/article/10.1186/s43008-020-00033-zCOX1COX2Oxford Nanopore technologiesPacBioRPB2Read placement |
| spellingShingle | 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. Johnston Paul M. Kirk Elaine Malosso Tom W. May Wieland Meyer Maarja Öpik Vincent Robert Marc Stadler Marco Thines Duong Vu Andrey M. Yurkov Ning Zhang Conrad L. Schoch Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus COX1 COX2 Oxford Nanopore technologies PacBio RPB2 Read placement |
| title | Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? |
| title_full | Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? |
| title_fullStr | Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? |
| title_full_unstemmed | Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? |
| title_short | Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? |
| title_sort | unambiguous identification of fungi where do we stand and how accurate and precise is fungal dna barcoding |
| topic | COX1 COX2 Oxford Nanopore technologies PacBio RPB2 Read placement |
| url | http://link.springer.com/article/10.1186/s43008-020-00033-z |
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