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A Genome Sequence for the Model Hemibiotroph Colletotrichum graminicola
L.J. Vaillancourt, L.J. Ma, M. Thon
Department of Plant Pathology
Fungal diseases cause enormous loses to agriculture worldwide each year, and are major barriers to food sustainability in the developing world. Elucidating the molecular mechanisms that regulate interactions between plants and fungal pathogens will be critical for future disease management. Complete genome sequences of pathogens and their hosts have become a key part of this research effort. The goal of this project is to release to the public a complete genome sequence for the model hemibiotrophic plant-pathogenic fungus Colletotrichum graminicola.
2009 Project Description
Fungi cause the vast majority of plant diseases and result in enormous losses to agriculture worldwide every year. There is a continual need to develop safer, more effective ways to combat plant disease. Elucidating molecular mechanisms that regulate interactions between plants and fungi will be critical for future disease management. Complete genome sequences of pathogens and of their hosts have become a key part of this research effort.
C. graminicola is a hemibiotrophic plant pathogen, which has aspects of both biotrophy and necrotrophy. Comparative studies of the genome of the model hemibiotroph C. graminicola with the genomes of these other classes may be very useful for elucidating functional and evolutionary relationships among these different pathogenicity types. Our goal for this project is to produce a high quality draft genome sequence of C. graminicola strain M1.001 and release that to the community on the Broad website. This would represent the first genome sequence for a member of this genus.
We have completed sequencing via a combination of Sanger and 454 protocols and have achieved approximately 8X genome coverage. The assembly covers 50.8 Mb, arranged in 653 scaffolds of 1151 contigs. The assembly has been validated with an optical map which demonstrated the presence of 13 chromosomes, including 3 "B-chromosomes" of less than 2 Mb in size. The assembly is currently available on the Broad database, together with reads from a second strain of C. graminicola from corn isolated from Brazil. The latter sequence data were donated to our project by Dupont Nemours Co.
The genome annotation is now underway, using a collection of ESTs generated by Sanger reads from both ends of 5000 clones from a normalized cDNA library generated from mycelium growing in complete medium, and 5000 clones from a non-normalized library growing in nitrogen starved conditions.