DNA sequence-based identification of Fusarium: A work in progress

Authors: O Donnell, Kerry; Whitaker, Briana; LARABA, IMANE - Orise Fellow; Proctor, Robert; Brown, Daren; Broders, Kirk; Kim, Hye-Seon; McCormick, Susan; Busman, Mark; AOKI, TAKAYUKE - National Agriculture And Food Research Organization (NARO), Agricultrual Research Center; TORRES-CRUZ, TERRY - Pennsylvania State University; GEISER, DAVID - Pennsylvania State University

Submitted to: Plant Disease
Publication Type: Review Article
Publication Acceptance Date: 12/9/2021
Publication Date: 5/10/2022
Citation: O'Donnell, K., Whitaker, B.K., Laraba, I., Proctor, R.H., Brown, D.W., Broders, K., Kim, H.-S., McCormick, S.P., Busman, M., Aoki, T., Torres-Cruz, T.J., Geiser, D.M. 2022. DNA sequence-based identification of Fusarium: A work in progress. Plant Disease. 106(6):1597-1609. https://doi.org/10.1094/PDIS-09-21-2035-SR.
DOI: https://doi.org/10.1094/PDIS-09-21-2035-SR

Interpretive Summary: Members of the mold genus Fusarium are the most important group of toxin-producing plant pathogens. They are responsible for multibillion U.S. dollar annual losses to the world’s agricultural economy due to reduction in yields, price discounts, and toxin contaminated food and feed that is unsuitable for consumption by humans and animals. Accurate species-level identification of these pathogens is crucial for disease diagnosis and management because knowing their identity connects it with what is known about the pathogen’s host range, geographic distribution, and toxin production potential. This can be a daunting task because this agriculturally important genus is currently estimated to comprise well over 400 genetically distinct species and because morphology cannot be used to accurately identify most of these species. To address the critical need for accurate pathogen identification, we have populated FUSARIUM-ID v.3.0 (http://isolate.fusariumdb.org/) with DNA sequence data from portions of three genes that resolve at or near the species level for the most important Fusarium species. Fusarium pathogens can be identified via the Internet by comparing a DNA sequence from an unknown with sequences in FUSARIUM-ID v.3.0. This research will be of interest to a wide range of scientists and quarantine officials charged with minimizing the threat these pathogens pose to global agricultural biosecurity and food safety.

Technical Abstract: Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists needing to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise over 400 phylogenetically distinct species (i.e., phylospecies), with over 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (NCBI GenBank and FUSARIUM-ID v.3.0) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1 and RPB2) that resolve at or near the species level for every Fusarium species. The objectives of this Special Report, and its companion (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.