Mycologia ISSN: 0027-5514 (Print) 1557-2536 (Online) Journal homepage: http://www.tandfonline.com/loi/umyc20 Sequence-based classification and identification of Fungi David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro, John W. Taylor & David M. Geiser To cite this article: David Hibbett, Kessy Abarenkov, Urmas Kõljalg, Maarja Öpik, Benli Chai, James Cole, Qiong Wang, Pedro Crous, Vincent Robert, Thorunn Helgason, Joshua R. Herr, Paul Kirk, Shiloh Lueschow, Kerry O’Donnell, R. Henrik Nilsson, Ryoko Oono, Conrad Schoch, Christopher Smyth, Donald M. Walker, Andrea Porras-Alfaro, John W. Taylor & David M. Geiser (2016) Sequence-based classification and identification of Fungi, Mycologia, 108:6, 1049-1068 To link to this article: https://doi.org/10.3852/16-130 © 2016 by The Mycological Society of America Published online: 30 Jan 2017. Submit your article to this journal Article views: 9271 View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=umyc20 Mycologia, 108(6), 2016, pp. 1049–1068. DOI: 10.3852/16-130 # 2016 by The Mycological Society of America, Lawrence, KS 66044-8897 Issued 25 January 2017 Sequence-based classification and identification of Fungi David Hibbett1 Christopher Smyth Biology Department, Clark University, Worcester, Department of Plant Pathology and Environmental Massachusetts 01610 Microbiology, 121 Buckhout Laboratory, Penn State University, University Park, Pennsylvania 16802 Kessy Abarenkov Urmas Kõljalg Donald M. Walker Maarja Öpik Department of Biology, Tennessee Technological University, Institute of Ecology and Earth Sciences, 1100 N. Dixie Ave., Cookeville, Tennessee 38505 University of Tartu, 40 Lai St, Tartu 51005, Estonia Andrea Porras-Alfaro Benli Chai Department of Biological Sciences, Western Illinois University, James Cole Waggoner Hall 372, 1 University Circle Macomb, Illinois 61455 Qiong Wang Department of Plant, Soil, and Microbial Sciences, John W. Taylor Michigan State University, Plant and Soil Sciences University of California, Department of Plant and Microbial Building, 1066 Bogue St. Room 540, East Lansing, Biology, 111 Koshland Hall, Berkeley, California 94720 Michigan 48824 David M. Geiser Pedro Crous Department of Plant Pathology and Environmental Vincent Robert Microbiology, 121 Buckhout Laboratory, Penn State Centraalbureau voor Schimmelcultures Fungal Biodiversity University, University Park, Pennsylvania 16802 Centre (CBS-KNAW), 3508 AD, Utrecht, the Netherlands Abstract: Thorunn Helgason Fungal taxonomy and ecology have been Department of Biology, University of York, revolutionized by the application of molecular meth- York YO10 5DD, United Kingdom ods and both have increasing connections to genomics and functional biology. However, data streams from Joshua R. Herr traditional specimen- and culture-based systematics Department of Plant Pathology and Center for Plant Science Innovation, University of Nebraska, are not yet fully integrated with those from metage- Lincoln, Nebraska 68503 nomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and meta‐ Paul Kirk bolic properties of fungal communities. This article Biodiversity Informatics and Spatial Analysis, Royal Botanic Gardens, Kew, Surrey TW9 3AF, United Kingdom reviews current resources, needs, and opportunities for sequence-based classification and identification Shiloh Lueschow (SBCI) in fungi as well as related efforts in prokaryotes. Kerry O’Donnell To realize the full potential of fungal SBCI it will be NCAUR ARS USDA, 1815 N. University St., Peoria, necessary to make advances in multiple areas. Improve- Illinois 61604 ments in sequencing methods, including long-read and R. Henrik Nilsson single-cell technologies, will empower fungal molecu- University of Gothenburg, Department of Biological and lar ecologists to look beyond ITS and current shotgun Environmental Sciences, Box 461, 405 30 Göteborg, metagenomics approaches. Data quality and accessibil- Sweden ity will be enhanced by attention to data and metadata Ryoko Oono standards and rigorous enforcement of policies for Department of Ecology, Evolution, and Marine Biology, deposition of data and workflows. Taxonomic commu- University of California Santa Barbara, Santa Barbara, nities will need to develop best practices for molecular California 93106 characterization in their focal clades, while also con- Conrad Schoch tributing to globally useful datasets including ITS. National Center for Biotechnology Information, National Changes to nomenclatural rules are needed to enable Library of Medicine, National Institutes of Health, Bethesda, valid publication of sequence-based taxon descriptions. Maryland 20892 Finally, cultural shifts are necessary to promote adop- tion of SBCI and to accord professional credit to indivi- duals who contribute to community resources. Submitted 25 Jun 2016; accepted for publication 29 Sep 2016. Key words: biodiversity informatics, metagenomics, 1 Corresponding author. E-mail: [email protected] molecular ecology, nomenclature, systematics, taxonomy 1049 Published online 30 Jan 2017 1050 MYCOLOGIA TABLE I. Terms and concepts for sequence-based classification and identification Candidatus A provisional taxonomic category for prokaryotes that lack a type culture Environmental nucleic acid species (ENAS) A species recognized solely with environmental molecular sequences Environmental sequence A DNA or RNA sequence obtained directly from a microbial community using amplicon or shotgun methods Molecular operational taxonomic unit (MOTU) An unranked taxonomic entity recognized with environmental sequences Nomenclature The set of rules detailed in the ICNAFP that determine the correct name for algae, fungi, and plants Sequence-based classification (SBC) The process by which species are discovered, named, and classified according to their phylogenetic relationships. Sequence-based identification (SBI) The process by which the products of taxonomy are used to identify individuals and determine the composition of communities with reference to existing classifications Species hypotheses (SH) A term coined to describe taxa whose ITS rRNA gene sequences cluster at user-defined cutoff levels i.e. 97–99% Taxonomy The branch of science focused on naming, describing, and classifying all forms of life Virtual taxa (VT) Phylogenetically defined sequence groups that roughly correspond to species INTRODUCTION Analyses of environmental DNA and RNA sequences may involve two complementary but distinct activities: Fungi make up an underdescribed, poorly documen- Sequence-based classification (SBC) and sequence-based ted clade of eukaryotes that have immense ecological identification (SBI) (Herr et al. 2015). The goals of SBC and economic impacts. Many fungi are microscopic are to discover, name, and classify fungal species accord- or have cryptic life cycles that make detection difficult. ing to their phylogenetic relationships. In contrast, SBI Approximately 135 000 species of fungi have been uses the products of taxonomy to identify individuals described, but the actual diversity of the group is likely and determine the composition of fungal communities to be in the millions of species (Blackwell 2011, Taylor with reference to existing classifications. SBI is a central et al. 2014). Investigations into fungal diversity have element of ecological studies, including metatranscrip- traditionally been based on fruiting bodies or cultures, tomic studies of community-level metabolic processes. but an increasing number of studies that obtain DNA Collectively, sequence-based classification and identifica- “ ” and RNA sequences directly from environmental tion (SBCI) denotes the full range of activities required — sources such as soil, water, air, or tissues of other to detect and characterize fungi in the environment — organisms are revealing potentially new fungal spe- based on nucleic acid sequences (TABLE I). cies at dramatically accelerated rates (Hibbett et al. New resources for SBCI are required to fully 2011, Lindahl et al. 2013). For example, the Cryptomy- exploit the staggering volume of data flowing from fun- cota (Rozellomycota, rozellida) (Lara et al. 2010, Jones gal molecular ecology studies using high-throughput et al. 2011, Corsaro et al. 2014) and Archaeorhizomy- sequencing technologies. Huge numbers of undescribed cetes are major clades of Fungi that are known almost taxa known only from environmental sequences need to entirely from environmental DNA sequences (Rosling be classified and linked to phenotypic, ecological, and et al. 2011, James and Berbee 2012). Many environmen- functional traits. This article aims to: (i) envision the tal sequences can only be identified to the level of a potential of SBCI and identify its conceptual challenges; phylum or simply “fungi” (Nilsson et al. 2016), even in (ii) survey current resources for SBCI in fungi and sophisticated analyses that use rigorous phylogenetic assess their strengths, limitations, and opportunities for methods and that consider ribosomal RNA (rRNA) sec- enhancement; and (iii) consider options for integrating ondary structure (Glass et al. 2013). Thus, it is likely sequence-based fungal species into taxonomic systems