Sequencing Ustilago maydis
The Ustilago maydis sequence project is part of the Broad Institute's Fungal Genome Initiative and was accomplished through collaborations with the Broad Institute, Bayer CropScience AG and Exelixis, Inc. The goal of this project is to release 10X genomic coverage for U. maydis strain 521. Bayer CropScience contributed their low-coverage genome sequence of U. maydis strain 521. These data consist of 17.4 Mb in 28 contigs and were generated from a minimal tiling path of overlapping BAC clones that cover 23 chromosomes. Exelixis has provided 5X whole-genome shotgun sequences of U. maydis strain FB1 that is assembled and aligned against the WGS assembly of strain 521 to identify polymorphism between these two strains. The collaborators for this project also include:
Dr. Scott Gold, Plant Pathology University of Georgia, USA
Dr. James Kronstad, University of British Columbia, Canada
Dr. Flora Banuett, Biological Sciences California State University
Dr. Joerg Kaemper, MPI für Terrestrische Mikrobiologie, Germany
Dr. Regine Kahmann, MPI für Terrestrische Mikrobiologie, Germany
Bayer CropScience and Dr. Barry Saville at University of Toronto also contributed 15,389 ESTs of strain 521 to aid the annotation of the U. maydis genome.
Our specific aims are to:
- Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome
- Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience
- Perform automated annotation of the sequence assembly
- Align the strain 521 assembly with the FB1 assembly provided by Exelixis
- Release the sequence assembly and results of our annotation and analysis to public
Questions about the project should be directed to annotation-webmaster(at)broad.mit.edu.
June 2003 - Release 1 consists of a 10X whole-genome shotgun assembly generated at Broad and an alignment between this assembly and Bayer's physical map.
March 2004 - Release 2 consists provide the results of automated genome annotation and visualization of alignment between strain 521 and FB1.
What is Ustilago maydis?
Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection.
Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi.
Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans.
Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production.
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