The Fungal Genome Initiative (FGI) produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. Over 25 fungi have been sequenced or are being sequenced, including human and plant pathogens as well as fungi that serve as basic models for molecular and cellular biology.

The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes being governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers not only the value of data from each organism given their role in basic research, health, agriculture, and industry, but also their value in comparative genomics.

Many of the fungi being sequenced comprise clusters of closely related organisms. By comparing sequence from one genome to another and correlating genomic differences with phenotypic differences, such as pathogenicity or production of drugs, scientists may be able to narrow the search for genes and regions that underlie important behaviors.

The FGI has been supported by the National Human Genome Research Institute, the National Science Foundation, the National Institute of Allergy and Infectious Disease, and the US Department of Agriculture.

Bruce Birren, co-director of the Genome Analysis Program and director of the Microbial Sequencing Center, leads the Fungal Genome Initiative. James Galagan, associate director of the Microbial Genome Analysis, is responsible for developing and applying computational tools and methods for FGI annotation and analysis. Christina Cuomo, research scientist, and Li-Jun Ma, research scientist, are responsible for managing FGI genome sequencing and analysis projects. Matthew Henn, research scientist, is responsible for scientific and project development. Keri Devon, senior scientific project manager, is responsible for organizational development and project management.