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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #331169
Research Project: Genomic and Metabolomic Approaches for Detection and Control of Fusarium, Fumonisins and Other Mycotoxins on Corn

Location: Mycotoxin Prevention and Applied Microbiology Research

Title: Sequence-based classification and identification of fungi

Author
item HIBBETT, DAVID - Clark University
item ABARENKOV, KESSY - University Of Tartu
item KOLJALG, URMAS - University Of Tartu
item OPIK, MAARJA - University Of Tartu
item CHAI, BENLI - Michigan State University
item COLE, JAMES - Michigan State University
item WANG, QIONG - Michigan State University
item CROUS, PEDRO - Fungal Biodiversity
item ROBERT, VINCENT - Fungal Biodiversity
item O Donnell, Kerry

Submitted to: Mycologia
Publication Type: Other
Publication Acceptance Date: 9/29/2016
Publication Date: 1/30/2017
Citation: Hibbett, D., Abarenkov, K., Koljalg, U., Opik, M., Chai, B., Cole, J., Wang, Q., Crous, P., Robert, V., O Donnell, K., et al. 2017. Sequence-based classification and identification of fungi. Mycologia. 108(6):1049-1068.
DOI: https://doi.org/10.3852/16-130

Interpretive Summary:

Technical 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 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.