Fusarium MLST database

May 15, 2010

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories.  The database comprises partial sequences from three nuclear genes: translation elongation factor 1α (EF-1α), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2).  These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium.  Phylogenetic analyses of the combined dataset reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate’s clade membership and genetic diversity. To identify isolates to species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is web-accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the CBS-KNAW Fungal Biodiversity Center (http://www.cbs.knaw.nl/Fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit cultures of novel mycosis-associated fusaria in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center), along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

Searching and Identification

May 15, 2010

The Fusarium MLST website hosted by the CBS-KNAW Fungal Biodiversity Centre allows one to access a database of 1365 well studied isolates and 2692 associated sequences from the following regions: Translation elongation factor 1 alpha gene (EF1), RNA polymerase I beta subunit gene (RPB1), RNA polymerase II beta subunit gene (RPB2), Calmodulin gene (CAL), beta-tubulin gene (TUBB), Histone gene, IGS, Internal transcribed spacers (ITS1 and ITS2), 28S ribosomal RNA large subunit (28S - LSU) and Mitochondrial gene. It must be noted that, for the time being, only a small portion of the strains have been sequenced for all the genes. In Fusarium chlamydosporum species complex, EF1, RPB2, CAL, ITS and LSU sequences are available. For Fusarium dimerum species complex, EF1, TUBB, ITS and LSU are most of the time present. Strains belonging to Fusarium incarnatum-equiseti species complex have been sequenced for EF1, RPB2, CAL, ITS and LSU. Fusarium oxysporum species complex is well represented in terms of strains but only a few EF1, and LSU are more or less consistently present while TUBB as well as ITS have been sequenced in a few cases. For Fusarium solani species complex, several genes (EF1, RPB2, CAL, TUBB, ITS and LSU) are represented but few strains have been sequenced for all of them. Finally, Gibberella fujikuroi species complex have been well studied and most strains have data for EF1, CAL, TUBB, Histone, IGS, ITS, LSU and Mitochondrial gene.   

Simple and advanced queries on the strains table are possible via a user-friendly interface.

For the identification, two major options are possible. The first one is the Single sequence alignment algorithm comparing a unique unknown sequence against the ones present in our Fusarium MLST sequences reference database. It’s also possible to compare it against all fungal sequences available from both Genbank and the CBS-KNAW sequences database (see how it works here). The second option (Multiple sequences) allows the alignment of several sequences of several loci at the same time against the Fusarium MLST database using the polyphasic comparison tools of the BioloMICS software. Since not all the sequences  are available for all the strains, comparisons will be based on unequal datasets and might lead to unbalanced identifications. This being said, these multi-locus sequences comparisons are extremely powerful and usually allow more reliable identifications (see how it works here).

People involved in the Fusarium MLST project

May 11, 2010

Kerry O’Donnell1*†, Deanna A. Sutton2, Michael G. Rinaldi2, Brice A. J. Sarver3, S. Arunmozhi Balajee4, Hans-Josef Schroers5, Richard C. Summerbell6, Vincent A. R. G. Robert7, Pedro W. Crous7, Ning Zhang8, Takayuki Aoki9, Kyongyong Jung10, Jongsun Park10, Yong-Hwan Lee10, Seogchan Kang11, Bongsoo Park11, and David M. Geiser11

Bacterial Foodborne Pathogens and Mycology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, Illinois1; Department of Pathology, University of Texas Health Science Center, San Antonio, Texas2; Department of Biological Sciences, University of Idaho, Moscow, Idaho3; Centers for Disease Control and Prevention, Atlanta, Georgia4; Agricultural Institute of Slovenia, Ljubljana, Slovenia5; Sporometrics Inc., Toronto, Canada6; CBS-KNAW Fungal Biodiversity Center, Utrecht, the Netherlands7; Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey8; NIAS Genebank (MAFF), National Institute of Agrobiological Sciences, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602 Japan9; Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea10; and Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania11

Phylogenetic tree

May 11, 2010

Corresponding Authors

For Fusarium related maters:

Kerry O’Donnell

Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, 1815 North University Street, Peoria, IL 61604-3999, USA

Phone: (309) 681-6383, Fax: (309) 681-6672

E-mail: kerry.odonnell@ars.usda.gov

For software and website related maters:

Vincent A. Robert

CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, Utrecht, The Netherlands

E-mail: v.robert@cbs.knaw.nl