Skip to main content
ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #317287

Title: Fusarium MLST database

item CROUS, PEDRO - Fungal Biodiversity
item ROBERT, VINCENT A.R. - Fungal Biodiversity
item LOMBARD, LORENZO - Fungal Biodiversity
item GIRALDO, ALEJANDRA - Fungal Biodiversity
item VAN DIEPENINGEN, ANNE - Fungal Biodiversity
item O Donnell, Kerry
item Ward, Todd
item GEISER, DAVID - Pennsylvania State University
item KANG, SEOGCHAN - Pennsylvania State University

Submitted to: Electronic Publication
Publication Type: Other
Publication Acceptance Date: 5/15/2015
Publication Date: 1/15/2016
Citation: Crous, P.W., Robert, V.A.R.G., Lombard, L., Giraldo, A., van Diepeningen, A., O'Donnell, K., Ward, T.J., Geiser, D.M., Kang, S. 2016. Fusarium MLST database. Electronic Publication. Available:

Interpretive Summary:

Technical Abstract: The CBS-KNAW Fungal Biodiversity Centre’s Fusarium MLST website (, and the corresponding Fusarium-ID site hosted at the Pennsylvania State University (; Geiser et al. 2004, Park et al. 2010) were constructed to facilitate identification of agriculturally and medically important fusaria by conducting nucleotide BLAST queries of these dedicated DNA sequence databases via the Internet. As one of the world’s most important mycotoxin-producing plant pathogens and emergent human opportunistic pathogens (Balajee et al. 2009, Geiser et al. 2013), disease management and infection control require that these economically destructive fungi be identified accurately and rapidly (Wingfield et al. 2012). However, numerous molecular phylogenetic studies over the past two decades (see References) have established that morphological species recognition frequently fails to distinguish many fusaria that have been discovered employing genealogical concordance phylogenetic species recognition (GCPSR sensu Taylor et al. 2000). When it was released in 2004 (Geiser et al. 2004), Fusarium-ID was populated initially with partial translation elongation factor 1-a (TEF1) sequences, which can be used to identify most but not all fusaria. To address this shortcoming, a concerted effort has and will continue to be made to populate the Fusarium-ID (Park et al. 2010) and Fusarium MLST databases with partial sequences from two additional phylogenetically informative loci, DNA-directed RNA polymerase II largest (RPB1) and second largest subunit (RPB2). Work in progress is directed at populating these databases with portions of these three genes from the ~300 phylogenetically distinct fusaria discovered to date via GCPSR. These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium (O’Donnell et al. 2010) (see the section on Searching and Identification below for the other loci currently available in Fusarium MLST). Looking to the future, other phylogenetically informative, orthologous genes will be added to both databases that resolve at or near the species-level and can be used across the phylogenetic breadth of Fusarium. A robust phylogeny of the genus inferred from partial RPB1+RPB2 sequence data resolved 20 monophyletic species complexes and nine monotypic lineages, which were named informally to facilitate communication of an isolate’s clade membership and genetic diversity (Fig. 1, O’Donnell et al. 2013). Researchers interested in obtaining reference strains should contact the CBS-KNAW Biodiversity Centre (, which houses a large collection of phylogenetically diverse fusaria.