The Sclerotinia sclerotiorum 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 and Fosmids and assembled using 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:
- Produce a high quality draft assembly of the S. sclerotiorum genome with an average depth of ~7-fold in Q20 bases and ~40-fold physical coverage in the assembly
- Sequence 12,000 cDNAs from two libraries to increase the accuracy of the S. sclerotiorum annotation
- Perform automated annotation of the S. sclerotiorum assembly including gene calling, functional annotation, and protein domain identification
- Immediately release all the information to public.
Our collaborators for the S. sclerotiorum genome project are:
- Dr. Martin B. Dickman, University of Nebraska
- Dr. Linda Kohn, University of Toronto
- Dr. Jeffrey Rollins, University of Florida
The genomic DNA for shotgun sequencing and cDNA libraries were provided by Jeffrey Rollins.
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 firstname.lastname@example.org.
What is Sclerotinia sclerotiorum?
Sclerotinia sclerotiorum (Lib.) de Bary is among the world's most successful and omnivorous fungal plant pathogens, with a host range of greater than 400 plant species. Despite decades of dedicated effort, resistant germplasm is still lacking in economically important crops. As an exemplar of soilborne pathogens and necrotrophic pathogenesis, S. sclerotiorum is a model for development of asexual, persistant propagules, somatic compatibility, and sexual sporulation. It is also central to a group of Ascomycetes with poorly known evolutionary relationships. We foresee control measures on several scales, e.g., blocking pathogen-plant signaling, defeating key pathogen developmental stages; or maintaining a broad base of genetic resistance against a range pathogen genotypes. These strategies could also be effective against closely related species. In the longer term, we see comparative genomics as tool for getting at key processes controlling genetic stability in populations, basic principals of pathogenesis in comparisons among other fungi, and better resolution of the Ascomycete branches (> 30, 000 species) of the Tree of Life.
Which strain is sequenced?
The strain chosen for sequencing is designated as the '1980' strain (ATCC18683).