DNA sequence-based identification of Fusarium: Current status and future directions

Authors: O Donnell, Kerry; Ward, Todd; ROBERT, VINCENT A.R. - Fungal Biodiversity; CROUS, PEDRO - Fungal Biodiversity; GEISER, DAVID - Pennsylvania State University; KANG, SEOGCHAN - Pennsylvania State University

Submitted to: Phytoparasitica
Publication Type: Review Article
Publication Acceptance Date: 8/20/2015
Publication Date: 11/1/2015
Publication URL: https://handle.nal.usda.gov/10113/5642473
Citation: O'Donnell, K., Ward, T.J., Robert, V.A.R.G., Crous, P.W., Geiser, D.M., Kang, S. 2015. DNA sequence-based identification of Fusarium: Current status and future directions. Phytoparasitica. 43(5):583-595.

Interpretive Summary: This invited mini-review is intended to provide a detailed introduction on how to identify unknown isolates of the filamentous fungus Fusarium using DNA sequence data from portions of 1-to-3 genetically informative genes. A simple step-by-step guide is provided to help end-users optimize their chances of obtaining an accurate species-level identification when they conduct searches one or more of the following three web-accessible databases: FUSARIUM-ID (http://isolate.fusariumdb.org/), Fusarium MLST (http://www.cbs.knaw.nl/fusarium/) and NCBI GenBank (http://www.ncbi.nlm.nih.gov/). FUSARIUM-ID and Fusarium MLST are dedicated to web-based identification of Fusarium and contain extensively curated sequences from vouchered strains that can be ordered online. By contrast, GenBank houses uncurated sequences, many of which are misidentified, so successfully navigating NCBI presents special challenges that are discussed herein. Given that Fusarium ranks as one of the most important toxin producing plant pathogens and opportunistic pathogen of humans whose immune systems are impaired, infection control, and disease management are heavily reliant on the rapid and accurate identification of the pathogenic species. These databases will be continuously populated with sequences as novel pathogens and toxigenic species are discovered so that agricultural and medical scientists worldwide can identify them rapidly via the Internet.

Technical Abstract: Fusarium easily ranks as one of the most important mycotoxigenic plant pathogens and emergent opportunistic pathogen of immunologically impaired humans. Informed disease management and infection control are heavily reliant on an accurate identification of the toxigenic and/or etiological agent. However, numerous studies over the past two decades that employed phylogenetic species recognition based on genealogical concordance and non-discordance of multilocus DNA sequence data have firmly established that morphological species recognition frequently fails within Fusarium. To meet the growing needs of the global Fusarium community, two dedicated web-accessible databases, FUSARIUM-ID (http://isolate.fusariumdb.org/) and Fusarium MLST (http://www.cbs.knaw.nl/fusarium/), were constructed at the Pennsylvania State University and the CBS-KNAW Biodiversity Centre, respectively, to facilitate species identifications employing nucleotide BLAST queries via the Internet. Of the marker loci targeted to date, partial sequences from translation elongation factor-1a (TEF1), and DNA-directed RNA polymerase II largest (RPB1) and second largest subunit (RPB2) have proven to be the most useful. The primary focus of this mini-review is to provide a simple step-by-step guide to increase the odds of obtaining an accurate species-level identification using FUSARIUM-ID, Fusarium MLST, and NCBI GenBank (http://www.ncbi.nlm.nih.gov/). Navigating the latter database is particularly challenging because it houses many misidentified Fusarium sequences, which we attribute to the open deposit of uncurated sequences. Looking to the future, our goal is to identify additional genes as informative as TEF1, RPB1, and RPB2 from genome-scale data to advance Fusarium identification, molecular diagnostics, and phylogenetic inference.