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-AlfaroJohn W. Taylor, David M. Geiser

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Pages (from-to)1049-1068
Number of pages20
JournalMycologia
Volume108
Issue number6
DOIs
StatePublished - Nov 1 2016

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All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Hibbett, D., Abarenkov, K., Kõljalg, U., Öpik, M., Chai, B., Cole, J., Wang, Q., Crous, P., Robert, V., Helgason, T., Herr, J. R., Kirk, P., Lueschow, S., O’Donnell, K., Nilsson, R. H., Oono, R., Schoch, C., Smyth, C., Walker, D. M., ... Geiser, D. M. (2016). Sequence-based classification and identification of Fungi. Mycologia, 108(6), 1049-1068. https://doi.org/10.3852/16-130