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FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification
Terry J Torres-Cruz1, Briana K Whitaker2, Robert H Proctor2
1Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A.
Abstract:
Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.
Insights
Accurate identification of Fusarium species is crucial for agriculture and health. FUSARIUM-ID v.3.0 enhances species identification using the translation elongation factor 1-alpha (TEF1) gene and improved data accessibility.
Area of Science:
- Mycology
- Genomics
- Bioinformatics
Background:
- Fusarium species are significant agricultural, medical, and food safety concerns.
- Accurate Fusarium species identification typically relies on DNA sequence data.
- Previous FUSARIUM-ID database versions (v.1.0, v.2.0) had limitations in metadata and species representation.
Purpose of the Study:
- To present FUSARIUM-ID v.3.0, an improved database for Fusarium species identification.
- To address limitations of previous versions by enhancing data annotation and expanding taxon representation.
- To facilitate more accessible and accurate Fusarium species identification for researchers.
Main Methods:
- Development of FUSARIUM-ID v.3.0 with updated metadata annotation for sequences.
- Expansion of taxon representation in the translation elongation factor 1-alpha (TEF1) sequence database.
- Provision of a downloadable database file for local BLAST queries and a tutorial for various search software.
Main Results:
- FUSARIUM-ID v.3.0 offers improved metadata annotation and broader taxon coverage for TEF1 sequences.
- The database is now available as a downloadable file, enabling local BLAST searches.
- A tutorial is provided to guide users on performing local BLAST searches with different software.
Conclusions:
- FUSARIUM-ID v.3.0 represents a significant advancement for Fusarium species identification.
- The enhanced database and accessibility features will aid researchers in accurate species delineation.
- Regular updates are planned to incorporate new species and improve existing data.
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