title: Sequence-based classification and identification of Fungi.
abstract: 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 validPUBLICation 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.
authors.affiliation: a Biology Department, Clark University, Worcester, Massachusetts 01610.
authors.forename: David
authors.initials: D
authors.lastname: Hibbett
authors.forename: Kessy
authors.initials: K
authors.lastname: Abarenkov
authors.forename: Urmas
authors.initials: U
authors.lastname: Kõljalg
authors.affiliation: b Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu 51005, Estonia.
authors.forename: Maarja
authors.initials: M
authors.lastname: Öpik
authors.forename: Benli
authors.initials: B
authors.lastname: Chai
authors.forename: James
authors.initials: J
authors.lastname: Cole
authors.affiliation: c Department of Plant, Soil, and Microbial Sciences, Michigan State University, Plant and Soil Sciences Building, 1066 Bogue St. Room 540, East Lansing, Michigan 48824.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.forename: Pedro
authors.initials: P
authors.lastname: Crous
authors.affiliation: d Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW), 3508 AD, Utrecht, the Netherlands.
authors.forename: Vincent
authors.initials: V
authors.lastname: Robert
authors.affiliation: e Department of Biology, University of York, York YO10 5DD, United Kingdom.
authors.forename: Thorunn
authors.initials: T
authors.lastname: Helgason
authors.affiliation: f Department of Plant Pathology and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68503.
authors.forename: Joshua R
authors.initials: JR
authors.lastname: Herr
authors.affiliation: g Biodiversity Informatics and Spatial Analysis, Royal Botanic Gardens, Kew, Surrey TW9 3AF, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Kirk
authors.forename: Shiloh
authors.initials: S
authors.lastname: Lueschow
authors.affiliation: h NCAUR ARS USDA, 1815 N. University St., Peoria, Illinois 61604.
authors.forename: Kerry
authors.initials: K
authors.lastname: O'Donnell
authors.affiliation: i University of Gothenburg, Department of Biological and Environmental Sciences, Box 461, 405 30 Göteborg, Sweden.
authors.forename: R Henrik
authors.initials: RH
authors.lastname: Nilsson
authors.affiliation: j Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106.
authors.forename: Ryoko
authors.initials: R
authors.lastname: Oono
authors.affiliation: k National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892.
authors.forename: Conrad
authors.initials: C
authors.lastname: Schoch
authors.affiliation: l Department of Plant Pathology and Environmental Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802.
authors.forename: Christopher
authors.initials: C
authors.lastname: Smyth
authors.affiliation: m Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave., Cookeville, Tennessee 38505.
authors.forename: Donald M
authors.initials: DM
authors.lastname: Walker
authors.affiliation: n Department of Biological Sciences, Western Illinois University, Waggoner Hall 372, 1 University Circle Macomb, Illinois 61455.
authors.forename: Andrea
authors.initials: A
authors.lastname: Porras-Alfaro
authors.affiliation: o University of California, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, California 94720.
authors.forename: John W
authors.initials: JW
authors.lastname: Taylor
authors.affiliation: l Department of Plant Pathology and Environmental Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802.
authors.forename: David M
authors.initials: DM
authors.lastname: Geiser
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D005658:Fungi / Q000145:classification* / Q000235:genetics*; D056186:Metagenomics / Q000379:methods*; D010802:Phylogeny
keywords: biodiversity informatics; metagenomics; molecular ecology; nomenclature; systematics; taxonomy