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Project Information

The Puccinia graminis sequencing project is part of the Fungal Genome Initiative at the Broad Institute of MIT and Harvard. Its goal is to release a high quality draft genome assembly and automated annotation for Puccinia graminis tritici. Genomic DNA from strain CRL 75-36-700-3 was prepared from urediniospores (which are dikaryotic) by the Szabo group at the University of Minnesota. The genome size is estimated to be 80 Mb with a haploid chromosome number of 18.

Funding for the P. graminis sequencing project was provided by the National Science Foundation through the Microbial Genome Sequencing Program.

Our specific aims are as follows:

  • Generate 8X coverage of the P. graminis genome through whole genome shotgun sequencing and generate a high quality genome assembly.
  • Generate a physical fingerprint map using the shotgun Fosmid library.
  • Construct cDNA libraries from urediniospores, haustoria, uredinial hyphae, and pycnial/aecial tissues (from infected barberry). Sequence both ends of a total of 40,000 clones from these libraries.
  • Perform an automated annotation of the sequence assembly.
  • Develop and genetically map ~400 SNP markers.
  • Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of all sequence in GenBank.

Data Releases

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting 7X assembly was made public in January of 2007, and the results of automated genome annotation will be made public in future releases. Questions about the project should be directed to annotation webmaster.

Project Leadership

  • Les J. Szabo, USDA, ARS, Cereal Disease Laboratory, University of Minnesota
  • Christina Cuomo, Broad Institute of MIT and Harvard
  • Ralph Dean, North Carolina State University
  • Jacqueline Schein, British Columbia Cancer Agency Genome Sciences Centre

What is Puccinia graminis?

puccinia graminis

Puccinia graminis, the causal agent of stem rust, has caused serious disease of small cereal grains (wheat, barley, oat, and rye) worldwide. P. graminis is the first sequenced representative of the rust fungi (Uredinales), which are obligate plant pathogens. The rust fungi comprise more than 7000 species and are one of the most destructive groups of plant pathogens. Stem rust of wheat has been a serious problem wherever wheat is grown and has caused major epidemics in North America (1). In 1999, a new highly virulent race TTKS (Ug99) of P. graminis was identified in Uganda, and since then has spread, causing a widening epidemic in Kenya and Ethiopia (2). Due to its devastating ability to cause epidemics, P. graminis was developed as a biological warfare agent during the Cold War (3) and is now considered one of the most important potential agricultural bio-terrorism threats to U. S. agriculture (4).

Puccinia graminis is a heteroecious rust fungus with five spore stages and two hosts (5). The asexual stage (uredinial) infects cereal and grass hosts and is the economically important form of the pathogen. The sexual stage begins in the resting spore (teliospore) on leaves and stalks of the gramineous host. The sexual stage is completed on the aecial (alternate) host, barberry. P. graminis, as a species, has a broad host range that includes more than 300 species of cereals and grasses. Wheat stem rust, P. graminis f.sp. tritici is known to naturally infect 28 species belonging to eight genera, including wheat, barley and rye.

References

  1. A. P. Roelfs, in The Cereal Rusts Vol II. Diseases, Distribution, Epidemiology, and Control A. P. Roelfs, W. R. Bushnell, Eds. (Academic Press, Orlando, 1985) pp. 3-37.
  2. www.globalrust.org
  3. R. F. Line, C. S. Griffith, in Stem Rust of Wheat, From Ancient Enemy to Modern Foe P. D. Peterson, Ed. (APS Press, St. Paul, 2001) pp. 83-118.
  4. Public Health Security and Bio-terrorism Preparedness and Response Act (2002).
  5. K. J. Leonard, L. J. Szabo. 2005. Pathogen profile: Stem rust of small grains and grasses caused by Puccinia graminis. Molecular Plant Pathology 6:99-111.

Photo Captions and Credits

Photos on this page:

  1. Infected wheat stem with the uredinial stage of P. graminis. Courtesy of Charlie W. Barnes, University of Minnesota.
  2. P. graminis urediniospores, spore in bottom right corner stained to show germ pores. Courtesy of Yehoshua Anikster and Tamar Eilam, Tel Aviv University.
  3. P. graminis teliospores. Courtesy of Yehoshua Anikster and Tamar Eilam, Tel Aviv University.

Captions for the photos in the Home page (from left to right):

  1. Two-celled teliospores of Puccinia graminis f. sp. tritici, the cause of stem rust of wheat. Photo courtesy J. F. Hennen
  2. Aecium stage emerging from the lower surface of the Berberis leaf.  Courtesy of George J. Wong, University of Hawaii.
  3. P. graminis in the spermogonium stage. Courtesy of George J. Wong, University of Hawaii.
  4. P. graminis teliospores. Courtesy of Yehoshua Anikster and Tamar Eilam, Tel Aviv University.
  5. Wheat Stem Rust. Courtesy of the Agricultural Research Service, USDA.