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

Terry J. Torres-Cruz, Briana K. Whitaker, Robert H. Proctor, Kirk Broders, Imane Laraba, Hye Seon Kim, Daren W. Brown, Kerry O’Donnell, Tania L. Estrada-Rodríguez, Yong Hwan Lee, Kyeongchae Cheong, Emma C. Wallace, Chyanna T. McGee, Seogchan Kang, David M. Geiser

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

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 59 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.

Original languageEnglish (US)
Pages (from-to)1610-1616
Number of pages7
JournalPlant disease
Volume106
Issue number6
DOIs
StatePublished - Jun 2022

All Science Journal Classification (ASJC) codes

  • Agronomy and Crop Science
  • Plant Science

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