Sclerotinia sclerotiorum Genome Project

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Project Information

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 were 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.

Questions about the project should be directed to

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).

Data access and Citation

The genome assembly and annotation of Sclerotinia sclerotiorum is available in Genbank.

Data files formerly available on this website can be accessed on our fungal ftp site, and the genome can also be accessed in the JGI MycoCosm site and FungiDb.

EST data is available for developing sclerotia, mycelia at neutral pH, developing apothecia, stage 3 to 5 apothecia, infected Brassica napus (canola), infection cushions, tomato infection, and oxidative stress in the NCBI Trace Archive.

For use of this data, please cite: Amselem J et al., "Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.", PLoS Genet, 2011 Aug 18;7(8):e1002230