Fusarium comparative genome project

Project information

The Fusarium comparative genomics project sequenced multiple Fusarium genomes simultaneously to facilitate the comparative analysis among these closely related fungal species. The Fusarium comparative project is part of the Broad Fungal Genome Initiative and was funded by the U.S. Department of Agriculture's National Institute for Food and Agriculture.

Interactive website retirement

On 4/23/16 the Broad's Institute Fusarium comparative database and web site was retired due to expiration of funding and issues with maintaining the infrastructure. For many years we have been pleased to work closely with the fungal research community to create and support this resource. All data is available in NCBI, and integrated where possible into the JGI Mycocosm site and FungiDb.

The Fusarium Comparative Project

The genus Fusarium collectively represents the most important group of fungal plant pathogens, causing various diseases on nearly every economically important plant species. Of equal concern is the health hazard posed to humans and livestock by the plethora of Fusarium mycotoxins. Besides their economic importance, species of Fusarium also serve as key model organisms for biological and evolutionary research.

In 2002, the F. graminearum sequencing project was funded by the National Research Initiative, which is within the U.S. Department of Agriculture's National Institute for Food and Agriculture. The F. graminearum sequencing project represents a partnership between the Broad and the International Gibberella zeae Genomics Consortium (IGGR).

Continuing this effort, a Fusarium comparative project was funded through the same agency to improve gene annotation and to identify functional non-coding elements of F. graminearum. Two additional Fusarium species, F. oxysporum and F. verticillioides were selected to study evolutionary biology among these closely related but biologically distinct Fusarium species. These genomes are appropriately diverged from F. graminearum, while being important research platforms in their own right. F. oxysporum is a broad host range pathogen that has caused some of the world's most dramatic and economically devastating plant disease epidemics. Recently F. oxysporum has also emerged as a model for soil-borne fungal diseases with Arabidopsis and tomato as hosts. F. verticillioides is a cosmopolitan pathogen of maize and sorghum, and produces carcinogenic mycotoxins known as fumonisins.

A three-way comparison of F. oxysporum, F. verticillioides and F. graminearum offers powerful synergy in studies of pathogenicity and virulence factors, and their evolution within this genus.

Funding support from the United States Department of Agriculture, National Institute of Food and Agriculture. (Grant awards 2008-35600-04691, 2008-35604-18800 and MASR-2009-04374) made this release possible.

Genome dynamics of host specificity in the Fusarium oxysporum species complex

Members of the F. oxysporum species complex exhibit extraordinary genetic plasticity and cause some of the most destructive and intractable diseases across a diverse spectrum of hosts, including many economically important crops such as banana, cotton, canola, melons, and tomato. The primary solution to control such diseases is through the development of disease resistant plant cultivars. However, due to their persistence in the soil and the genetic plasticity of the organism, it is just a matter of time before the pathogen can adapt and overcome the newly deployed resistance. The Fusarium comparative genomics project highlighted the existence of lineage-specific chromosomes that are enriched for transposable elements and encode genes that are pathogenicity related. Empowering the high throughput and cost-effective sequence technologies and optical mapping, this project explored the genetic composition and evolutionary origin of lineage-specific chromosomes among a set of carefully selected strains, listed below, that capture the pathogenic and phenotypic diversity.

NRRL# Strain forma specialis Host


HDV247 pisi Pisum
32931 NRRL32931 (human) Homo
54002 Fo47 (biocontrol) Soil
54003 MN25 lycopersici race 3 Lycopersicum
54008 PHW808 conglutinans, race 2 Brassica/Arabidopsis
54005 PHW815 raphani Raphanus/Arabidopsis
26381 CL57 radicis-lycopersici Lycopersicum
54006 II5 cubense tropical race 4 Musa
26406   melonis Cucurbita
25433   vasinfectum Gossypium

The main collaborators of Fusarium comparative project

Dr. Corby Kistler at USDA, ARS Cereal Disease Lab of University of Minnesota
Dr. Jin-Rong Xu ant Purdue University
Dr. Frances Trail at Michigan State University
Dr. Seogchan Kang at Penn State University
Dr. Won-Bo Shim at Texas A&M University
Dr. Charles Woloshuk at Purdue University

Data Releases

March, 2007 - Release of the Fusaria Group site containg assembly and annotation of Fusarium verticillioides, Fusarium graminearum, and Fusarium oxysporum.

December, 2006 - Release of the automated annotation of Fusarium verticillioides

October, 2006 - Fusarium verticillioides Release 2. An 8X whole-genome shotgun assembly of F. verticillioides and the integration of the assembly to the existing genetic map. The assembly was deposited at Genbank under the project accession AIM01000000.

July, 2005 - Fusarium verticillioides Release 1. A 4X whole-genome shotgun assembly. The assembly was deposited at Genbank under the project accession AIM01000000.

Photo Credits

The photos on the front page come courtesy (left to right):

Frances Trail, Department of Plant Biology at Michigan State University
H. Corby Kistler, USDA, ARS Cereal Disease Lab and Department of Plant Pathology, University of Minnesota
Jin-Rong Xu, Department of Botany and Plant Pathology, Purdue University
Charles Woloshuk at Purdue University
H. Corby Kistler, USDA, ARS Cereal Disease Lab and Department of Plant Pathology, University of Minnesota

Data access and citation

The genome sequences of Fusarium are available in Genbank under bioproject PRJNA13839 (F. graminearum), PRJNA18813 (F. oxysporum), and PRJNA15553 (F. verticillioides); genomes are also available in the JGI Mycocosm site and in FungiDb. Data files formerly available on this website can be accessed on our fungal ftp site.

For use of this data please cite:

Ma LJ et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.

Cuomo CA et al. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science. 2007 Sep 7;317(5843):1400-2.