Research Accomplishment Reports 2010

A Genome Sequence for the Model Hemibiotroph Colletotrichum graminicola

L.J. Vaillancourt, L.J. Ma, M. Thon
Department of Plant Pathology

 

Non-Technical Summary

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.

2010 Project Description

We sequenced the genome of Colletotrichum graminicola strain M1.001 via a combination of Sanger and 454 protocols and achieved greater than 8X high quality genome coverage. The assembly covers 51.6 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 "mini-chromosomes" of less than 2 Mb in size. The genome was annotated with the aid of paired-end sequence from 10,000 cDNA clones, and it is predicted to contain approximately 12,000 genes. All the information is currently available on the Broad database, together with reads from a second strain of C. graminicola that was isolated from corn in Brazil. These sequence data were donated by Dupont Nemours Co.

In addition, genome data for a second species of Colletotrichum, C. higginsianum, will appear on the same Broad website which will become therefore a Colletotrichum comparative genome site. C. higginsianum is a pathogen of the model plant Arabidopsis and was sequenced independently by the Max Planck Institute in Cologne, Germany. The PI of the project agreed to have the Broad site host his data, and the Broad institute agreed to do so.

This will be a tremendous resource for the Colletotrichum community since C. graminicola can be considered the model for graminaceous Colletotrichum pathogens, while C. higginsianum can be considered the model for dicotyledonous Colletotrichum pathogens. Having both species on the same website and accessible using the same Broad tools and format will facilitate comparative analyses. Analysis of the genomes will continue, with a plan to develop a joint publication sometime in the next year.

2010 Impact

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 was 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 represents the first publicly available genome sequence for a member of this genus.