Project Information

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Additional information

Sequencing Fusarium graminearum

The F. graminearum sequencing project was funded by the National Research Initiative, which is within the U.S. Department of Agriculture's (USDA's) Cooperative State Research Education and Extension Service, and reviewed through the USDA/NSF Microbial Genome Sequencing Project. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated using paired end reads from plasmids, Fosmids and BACs and reassembled using improved Arachne (Batzoglou et al. 2002, Jaffe et al. 2003). The rapid availability of this sequence in an annotated form will immediately promote discovery of genes and potential anti-fungal targets, permit reconstruction of pathways, provide sequence-anchored clone paths for use in genetic and functional studies, and enable comparative genomic approaches to analysis.

Our specific aims are as follows:
  1. Generate and assemble Fusarium graminearum genome through whole genome shotgun sequencing.
  2. Integrate the genomic sequence with existing genetic map information.
  3. Perform automated annotation of the sequence assembly.
  4. Immediately release all the information to public.

The Fusarium graminearum genome project represents a partnership between the Broad Institute and the International Gibberella zeae Genomics Consortium (IGGR). The main collaborators of Fusarium genome project are:

Dr. Corby Kistler at USDA, ARS Cereal Disease Lab of University of Minnesota
Dr. Jin-Rong Xu at Purdue University
Dr. Frances Trail at Michigan State University

The Eli and Edythe L. Broad Institute is a partnership among MIT, Harvard and affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create the tools for genomic medicine and make them freely available to the world and to pioneer their application to the study and treatment of disease.

Questions about the project should be directed to annotation-webmaster@broad.mit.edu.

What is Fusarium graminearum?

Fusarium graminearum, the anamorph of Gibberella zeae, is the cause agency of head blight (scab) of wheat and barley that has emerged as the plant disease with the greatest impact on U.S. agriculture and society during the past decade. Approximately $3 billion have been lost to U. S. agriculture during wheat scab epidemics in the 1990s, having a devastating effect on farm communities in the upper Midwest and elsewhere (McMullen et al., 1997; Windels, 2000). Moreover, the disease is becoming a threat to the world's food supply due to recent head blight outbreaks in Asia, Canada, Europe and South America (Dubin et al., 1997). The fungus also infects and causes disease on corn and rice (Webster and Gunnell, 1992; White, 1999). The pathogen poses a two-fold threat: first, infested cereals are significantly reduced in seed quality and yield, and secondly, scabby grain is contaminated with trichothecene and estrogenic mycotoxins, making it unsuitable for food or feed (McMullen et al., 1997).

As a food safety issue, trichothecene toxins such as "vomitoxin" (deoxynivalenol) produced by this fungus pose a serious hazard to human and animal health because these sesquiterpenoids are potent inhibitors of eukaryotic protein biosynthesis. Vomitoxin causes weight loss and feeding refusal in non-ruminant livestock, and human ingestion of grain contaminated with F. graminearum has been associated with alimentary toxic aleukia as well as illness characterized by nausea, vomiting, anorexia, and convulsions (Murphy and Armstrong, 1995). Trichothecenes are also powerful modulators of human immune function and may promote neoplasms, cause autoimmune disease, or have long-term effects on resistance to infectious disease by altering immune response (Berek et al., 2001; Lindsay, 1997). Trichothecene producing Fusarium strains (the so-called "yellow rain" fungi) were reported to have been used as biological weapons in conflicts during the latter half of the 20th century (Wannemacher and Wiener, 1989) and were investigated by the U.S. Department of Defense as a potential cause of Gulf War Illnesses (Rostker, 2000). Potential environmental exposure of workers to trichothecenes in the agricultural and grain milling industries may soon be addressed as an occupational hazard.

Which strain is sequenced?

The strain chosen for sequencing by the International Gibberella zeae Genomics Consortium (IGGR) is designated PH-1 (NRRL 31084) and is a member of lineage 7 of Fusarium graminearum (Gibberella zeae). Lineage 7 is the predominant population of the wheat and barley scab fungus found in North America and Europe and is distributed worldwide (O'Donnell et al., 2000). Isolated in Michigan, PH-1 is highly fertile (Trail and Common, 2000), produces both mycotoxins, sporulates abundantly in pure culture and is highly pathogenic to wheat and barley. The strain can be readily transformed and is closely related to strain GZ3639 (NRRL 29169) that has been studied for trichothecene biosynthesis (Brown et al., 2001).

Data releases

The entire genome sequence has been deposited in GenBank with accession AACM00000000.

Release 1
High quality draft genome assembly
Release 2
Automated annotation, preliminary genome analysis and integration with genetic map

References

  1. Batzoglou, S., D. B. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger, J. P. Mesirov, and E. S. Lander. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Res 12: 177-89.
  2. Berek, L., I. B. Petri, A. A. Mesterhazy, J. Teren, and J. Molnar. 2001. Effects of mycotoxins on human immune functions in vitro. Toxicol. In Vitro 15:25-30.
  3. Brown, D. W., S. P. McCormick, N. J. Alexander, R. H. Proctor, and A. E. Desjardins. 2001. A genetic and biochemical approach to study trichothecene diversity in Fusarium sporotrichioides and Fusarium graminearum. Fungal Genet.Biol. 32:121-133.
  4. Dubin, H. J., L. Gilchrist, L. Reeves, and A. McNab. 1997. Fusarium Head Blight: Global Status and Prospects. CIMMYT, Mexico City.
  5. Jaffe, D. B., J. Butler, S. Gnerre, E. Mauceli, K. Lindblad-Toh, J. P. Mesirov, M. C. Zody, and E. S. Lander. 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13: 91-6.
  6. Lindsay, J. A. 1997. Chronic sequelae of foodborne disease. Emerg.Infect.Dis. 3:443-452.
  7. McMullen, M., R. Jones, and D. Gallenberg. 1997. Scab of wheat and barley: A re-emerging disease of devastating impact. Plant Dis. 81:1340-1348.
  8. Murphy, M. and D. Armstrong. 1995. Fusariosis in patients with neoplastic disease. Infect.Med. 12:66-67.
  9. O'Donnell, K., H. C. Kistler, B. K. Tacke, and H. H. Casper. 2000. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc.Natl.Acad.Sci.U.S.A 97:7905-7910.
  10. Rostker, B. 2000. Closeout Report, Biological Warfare Investigation, Gulf War Illnesses. http://www.gulflink.osd.mil/bw/index.html.
  11. Trail, F. and R. Common. 2000. Perithecial development by Gibberella zeae: a light microscopy study. Mycologia 92:130-138.
  12. Wannemacher, R. W. and S. L. Wiener. 1989. Trichothecene mycotoxins, p. 655-676. In: F. R. Sidell, E. T. Takafuji, and D. R. Franz (eds.), Medical Aspects of Chemical and Biological Warfare. Office of the Surgeon General at TMM Publications, Washington, DC.
  13. Ward, T.J., J.P. Bielawski, H.C. Kistler, E. Sullivan, and K. O'Donnell. 2002. Ancestral polymorphism and adaptive evolution in the trichothecene gene cluster of phytopathogenic Fusarium. Proc. Natl. Acad. Sci. U.S. A. 99:9278-9283.
  14. Webster, R. K. and P. S. Gunnell. 1992. Compendium of Rice Diseases. APS Press, The American Phytopathological Society, St. Paul, MN.
  15. White, D. G. 1999. Compendium of Corn Diseases. APS Press, The American Phytopathological Society, St. Paul, MN.
  16. Windels, C. E. 2000. Economic and social impacts of Fusarium head blight: Changing farms and rural communities in the Northern Great Plains. Phytopathology 90:17-21.