FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification

Authors: TORRES-CRUZ, TERRY - Pennsylvania State University; Whitaker, Briana; Proctor, Robert; Broders, Kirk; LARABA, IMANE - Orise Fellow; Kim, Hye-Seon; Brown, Daren; O Donnell, Kerry; ESTRADA-RODRIGUEZ, TANIA - Humboldt State University; LEE, YONG-HWAN - Seoul National University; CHEONG, KYEONGCHAE - Seoul National University; WALLACE, EMMA - Pennsylvania State University; MCGEE, CHYANNA - Pennsylvania State University; KANG, SEOGCHAN - Pennsylvania State University; GEISER, DAVID - Pennsylvania State University

Submitted to: Plant Disease
Publication Type: Database / Dataset
Publication Acceptance Date: 12/6/2021
Publication Date: 5/10/2022
Citation: Torres-Cruz, T.J., Whitaker, B.K., Proctor, R.H., Broders, K., Laraba, I., Kim, H.-S., Brown, D.W., O'Donnell, K., Estrada-Rodriguez, T.L., Lee, Y.-H., Cheong, K., Wallace, E.C., McGee, C.T., Kang, S., Geiser, D.M. 2022. FUSARIUM-ID v.3.0: An updated, downloadable resource for Fusarium species identification. Plant Disease. https://doi.org/10.1094/PDIS-09-21-2105-SR.
DOI: https://doi.org/10.1094/PDIS-09-21-2105-SR

Interpretive Summary: This study was conducted to expand the utility of FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php), a web-accessible DNA sequence database for the identification of Fusarium plant pathogens using partial DNA sequences from one or more informative genes. We created this website because Fusarium is the most important group of toxin-producing plant pathogens. These molds and their toxins are responsible for multibillion U.S. dollar losses to the world’s agricultural economy annually. Genetic analyses of Fusarium pathogens over the past 25 years have revealed that this genus comprises over 400 distinct species. Most of these species, however, can only be identified using DNA sequence data. Thus, we populated the updated version of this database, FUSARIUM-ID v.3.0, with DNA sequence data from portions of three informative genes that resolve at or near the species level for the most important toxigenic plant pathogens. The global phytopathology user community can identify their pathogens by comparing DNA sequence data from their isolates with those in FUSARIUM-ID v.3.0. We have also made it possible to download this database so that Fusarium pathogen identifications can be done locally on desktop computers using free software. FUSARIUM-ID will be updated on a regular basis as new DNA sequence data becomes available. Plant pathologists and other diverse applied scientists will greatly benefit from free access to this database, thereby promoting agriculture biosecurity worldwide.

Technical Abstract: FUSARIUM-ID is a publicly available database for the identification of Fusarium species using multiple marker loci, currently available through a web browser connected to a BLAST server (http://isolate.fusariumdb.org/blast.php). Although updated in 2010, FUSARIUM-ID had limitations related to downtime of the website, inconsistent metadata annotation for each sequence, and poor representation of some Fusarium species complexes and marker loci. Here we present FUSARIUM-ID v.3.0, which includes 1) additional and updated annotation of metadata for the isolate associated with each sequence, 2) expanded taxon representation in the TEF1 database, and most importantly, 3) availability of the database as a downloadable file that can be used to BLAST locally without the need of an external BLAST server. We also provide a tutorial file demonstrating how users can set up their desktop computers to perform local BLAST searches using free software (i.e., SequenceServer [Priyam et al. 2019], BLAST+ executable in the command line [Camacho et al. 2009], and Galaxy [www.usegalaxy.org]), as well as the proprietary Geneious software (https://www.geneious.com/). FUSARIUM-ID will be updated on a regular basis with additional sequences of TEF1 and other loci for representative species in the database and will also be updated with new and revised data and metadata.