Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

Journal Article · · Plant Disease
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [3];  [4];  [5];  [1];  [1];  [1];  [1]
  1. Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A.
  2. Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A.
  3. Department Natural Resources and Science, Humboldt State University, Arcata, CA 95521, U.S.A.
  4. Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
  5. Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
+ Show Author Affiliations

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.

Research Organization:
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
DOE Contract Number:
SC0014664
OSTI ID:
1982730
Journal Information:
Plant Disease, Vol. 106, Issue 6; ISSN 0191-2917
Publisher:
American Phytopathological Society
Country of Publication:
United States
Language:
English

References (33)

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases journal August 2019
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools journal November 2012
No to Neocosmospora : Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium journal October 2020
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update journal May 2018
Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex journal September 2021
Epitypification of Fusarium oxysporum – clearing the taxonomic chaos journal December 2019
Trends in Fungal Keratitis in the United States, 2001 to 2007 journal December 2010
DNA Sequence-Based Identification of Fusarium: A Work in Progress journal June 2022
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications journal October 2018
BLAST+: architecture and applications journal January 2009
Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing journal November 2010
Phylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin journal March 2019
Multiple evolutionary origins of the fungus causing Panama disease of banana: Concordant evidence from nuclear and mitochondrial gene genealogies journal March 1998
Resolving Fusarium: Current Status of the Genus journal August 2019
Population genetic structure and mycotoxin potential of the wheat crown rot and head blight pathogen Fusarium culmorum in Algeria journal June 2017
A Multilocus Genealogical Approach to Phylogenetic Species Recognition in the Model Eukaryote Neurospora journal December 2003
Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model journal March 2020
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi journal March 2012
Phylogenetic Species Recognition and Species Concepts in Fungi journal October 2000
FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium journal June 2004
Aflatoxins, fumonisins, and trichothecenes: a convergence of knowledge journal January 2013
MUSCLE: multiple sequence alignment with high accuracy and high throughput journal March 2004
Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium journal July 2020
Multiresistant Fusarium Pathogens on Plants and Humans: Solutions in (from) the Antifungal Pipeline? journal November 2019
DNA sequence-based identification of Fusarium: Current status and future directions journal September 2015
One Fungus, One Name: Defining the Genus Fusarium in a Scientifically Robust Way That Preserves Longstanding Use journal May 2013
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
Molecular systematics and phylogeography of the Gibberella fujikuroi species complex journal May 1998
Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex journal January 2021
Sequence-Based Identification of Aspergillus, Fusarium , and Mucorales Species in the Clinical Mycology Laboratory: Where Are We and Where Should We Go from Here? journal April 2009
The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes journal August 2010
Fusarium: more than a node or a foot-shaped basal cell journal March 2021
Biogeography and phylogeography of Fusarium: a review journal September 2010

Similar Records

Related Subjects

Plant Sciences