The Fungal Genomics group at the Broad Institute has sequenced and analyzed a wide diversity of fungal organisms that are important to medicine, agriculture and industry. Over 100 fungi have been sequenced, including human and plant pathogens as well as fungi that serve as basic models for molecular and cellular biology. Originally as the Fungal Genome Initiative, a partnership with the wider fungal research community, organisms are targeted 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.
Update for our website users
As of May 15 2015, we have initiated a process of retiring our older fungal genome websites. In many cases a project summary page will replace the former website, providing information on the project and links to genomic data in NCBI.
For many years we have been pleased to work closely with the respective fungal research communities to create and support these resources; we will continue to provide early public release of data on a new platform and at NCBI.
As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.
The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.
MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.
For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org
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.