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Sequence-based classification and identification of Fungi

Review article
Authors David Hibbett
Kessy Abarenkov
Urmas Koljalg
Maarja Opik
Benli Chai
James R Cole
Qiong Wang
Pedro W. Crous
Vincent A.R.G. Robert
Thorunn Helgason
Josh Herr
Paul Kirk
Shiloh Lueschow
Kerry O'Donnell
R. Henrik Nilsson
Ryoko Oono
Conrad L. Schoch
Christopher Smyth
Donny Walker
Andrea Porras-Alfaro
John W Taylor
David M. Geiser
Published in Mycologia
Volume 108
Issue 6
Pages 1049-1068
ISSN 0027-5514
Publication year 2016
Published at Department of Biological and Environmental Sciences
Pages 1049-1068
Language en
Keywords biodiversity informatics, metagenomics, molecular ecology, nomenclature, systematics, taxonomy
Subject categories Pathobiology, Soil biology, Forest Science, Biological Systematics, Ecology, Bioinformatics and Systems Biology, Botany, Microbiology, Bioinformatics (Computational Biology), Databases


Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

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