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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.
Acknowledgments
Preparation of this article was initiated in a 2 d workshop on SBCI in Fungi that was held at the Kellogg Center of Michigan State University, East Lansing, Michigan, 12–13 Jun 2014 (CitationHerr et al. 2015), which was supported by US National Science Foundation award No. DEB 1424740 to DG, AP-A, DSH, and JWT. A related symposium on “Sequence-based identification in Fungi” was held on 11 Jun 2014 at the annual meeting of the Mycological Society of America, and a Special Interest Group session on “Classifying, naming and communicating sequence based species” took place at the International Mycological Congress, 5 Aug 2014, Bangkok, Thailand. The authors thank Sam Kovaka, who performed the query of GenBank for species names (, Supplementary information), P. Brandon Matheny, and two anonymous reviewers for helpful comments. Mention of trade names or commercial products in thisPUBLICation is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the Victorian government or the US Department of Agriculture. USDA is an equal opportunity provider and employer. CLS acknowledges support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine. Mö acknowledges support from the Estonian Research Council (grant No. IUT20-28) and European Regional Development Fund (Centre of Excellence EcolChange). DSH acknowledges support of NSF award No. DEB-1208719.