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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND APPLICATION OF MOLECULAR PHYLOGENETICS OF FUNGI TO ENHANCE FOOD SAFETY AND FOOD SECURITY

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

Title: Fusarium identification databases, present and future

Authors
item Geiser, D - PENN STATE UNIV
item Kang, S - PENN STATE UNIV
item O Donnell, Kerry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: September 2, 2008
Publication Date: September 2, 2008
Citation: Geiser, D.M., Kang, S., O Donnell, K. 2008. Fusarium identification databases, present and future. Meeting Abstract.

Technical Abstract: DNA-sequence based identification of fungi is now in wide practice. For a community molecular identification tool to be effective, it must be based on an appropriately informative locus or set of loci, technology that is broadly available, and most importantly, connected to a definitive database. A first rudimentary attempt at creating such a database was FUSARIUM-ID (Geiser et al., Europ. J. Plant Pathol. 110:473-479, 2004). This database consists of a web-accessible BLAST server of partial translation elongation factor-1-alpha sequences. A key feature for this or any effective identification database is that all sequences be connected to vouchered, publicly available cultures. Shortcomings of the first version database include an incomplete representation of Fusarium species, a lack of accession data about isolates in the database, and an inability to download sequences. Here we outline features of a new Fusarium Database, which includes substantial improvements with regard to these shortcomings, as well as new features. The database, which is based on the PhytophthoraDB (http://www.phytophthoradb.org), will include identification tools for multiple loci attached to far more isolates. In addition, users will have access to isolate information, and be able to generate alignments, phylogenetic trees and virtual RFLP gels. New tools will allow users to link data from a query isolate to the released Fusarium genomes, and geographic information systems (GIS) functions.

Last Modified: 4/17/2014
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