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Project Information

The Stagonospora nodorum (Phaeosphaeria nodorum) sequencing project is part of the Broad Institute Fungal Genome Initiative. Its goal is to release an annotated assembly with 10X genome sequence coverage for Stagonospora nodorum strain SN15.

The Stagonospora nodorum genome project represents a partnership between the Broad Institute and the International Stagonospora nodorum Genomics Consortium (IGGR).

This Sequencing Project has been funded by the Australian Grains Research and Development Corporation and coordinated by the Australian Centre for Necrotrophic Fungal Pathogens. See http://wwwacnfp.murdoch.edu.au/ and http://www.grdc.com.au/ for further information.

The main collaborator of Stagonospora nodorum genome project is:
Dr. Richard Oliver at Murdoch University, South Street, WA, 6150, Australia

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.

Our specific aims are as follows:

  1. Generate and assemble sequence reads yielding 10X coverage of the S. nodorum genome through whole genome shotgun sequencing.
  2. Perform automated annotation of the sequence assembly.
  3. 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 the sequence assembly in GenBank.

Data Releases

We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. The resulting >10X assembly was made public on 4/15/2005, and the results of automated genome annotation will be made public in future releases.

Questions about the project should be directed to annotation-webmaster(at)broad.mit.edu.

What is Stagonospora nodorum?

 

General Description

Stagonospora nodorum is a filamentous ascomycete that is a major pathogen of wheat and related cereals. It is also known as Septoria nodorum and the disease is variously called glume blotch and Septoria (or Stagonospora) nodorum blotch (not to be confused with Septoria leaf blotch which is caused by Mycosphaerella graminicola). The sexual stage is important in the field and the teleomorph is called Phaeosphaeria nodorum.

Stagonospora causes major losses in wheat crops. In Australia, losses of $57M pa are considered typical. Almost all these losses are concentrated in the Western Australian wheat belt. It is a major pathogen in most other wheat growing regions. In some areas, such as parts of eastern, it renders wheat an uneconomic crop.

Stagonospora is a member of the Dothideomycetes, a class of fungi that includes many important plant pathogens such as Leptosphaeria, Ascochyta, Pyrenophora, Cochliobolus, Alternaria and Mycosphaerella. It is the first Dothideomycete genome sequence to be publicly released.

The lifecycle of Stagonospora comprises both sexual and asexual phases. The asexual spores are released from pycnidia and rain-splashed to initiate new infection foci. The pycnidiospores germinate on the surface of the leaf and penetrate through stomata and directly through the epidermal cell walls. Cell wall penetrations are often associated with simple swollen hyphopodia. Once inside, hyphae grow through the leaf blade. After a few days and when the leaf cells have largely collapsed, pycnidia are formed to complete the life cycle.

The macroscopic symptoms are lens-shaped lesions in which brown pycnidia develop in appropriate conditions. Lesions often form in stem nodes, hence the name "nodorum". The most damaging aspect of the disease is infection of the head, leading to the glume blotch symptoms. Sexual development takes place on stubble and takes several months. The fungus is heterothallic. Ascospores are released from pseudothecia and spread on the wind. Seed-borne transmission is also important. Stagonospora can be easily cultured in vitro on simple defined media. Gene manipulation techniques including gene replacement have been developed and are relatively straightforward. However, sexual crossing in the laboratory is problematic.

Pathogenicity has been studied through the analysis of the effects of disrupting the expression of a number of genes. A picture is emerging whereby pathogenicity is seen to be a tightly regulated process in which the fungus battles the plant to maximise both the speed and quantity of sporulation.

Significance

Stagonospora nodorum is both an important pathogen in its own right and a model for the dothideomycetes. The aim of the genome sequencing is to provide the community with the tools to analyse and dissect the genetic basis of pathogenicity. The goal is to understand the function of genes controlling all aspects of pathogenicity. This will lead to novel control methods, based on improved understanding of the lifecycle of the pathogenicity, new targets for chemical control and methods of enhanced plant defence.

Genome Facts

The haploid genome size of S. nodorum is estimated from the assembled genome sequence to be 37.1Mb. Pulsed field electrophoresis results have indicated that the genome comprises 14-19 chromosomes ranging from 0.4 to 3.5Mb. Strains differ markedly in their karyotype. This even applies to the progeny of a single ascus.

The sequenced strain is called SN15 and was collected in Western Australia. It is available from Richard Oliver (roliver(at)murdoch.edu.au) or the FGSC.

This Sequencing Project has been funded by the Australian Grains Research and Development Corporation and coordinated by the Australian Centre for Necrotrophic Fungal Pathogens. See http://wwwacnfp.murdoch.edu.au/ and http://www.grdc.com.au/ for further information.


Photo Credits

We would like to thank the following sources for the use of the images on the home page (from left to right):

  1. USDA (United States Department of Agriculture)
  2. HGCA
  3. Cornell University
  4. and 5.: UGA (University of Georgia) Warnell School of Forestry