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Genomics is a powerful and quickly evolving tool to understand processes of host-pathogen interactions. The Fungal Genomics Program (jgi.doe.gov/fungi) of the US Department of Energy (DOE) Joint Genome Institute (JGI) is partnering with international scientific community to explore the diversity of fungal plant pathogens and their interactions with plant hosts by offering several large scale genomics initiatives. Within one of these initiatives, the <i>Genomic Encyclopedia of Fungi</i>, we explore the interactions between bioenergy crop species with symbionts and pathogens.  Another, the <i>1000 Fungal Genomes</i> project, is aimed to explore diversity across the Fungal Tree of Life in order to provide references for every family of fungi and a solid basis for environmental metagenomics.  Open to all scientists around the world, these initiatives result in massive amounts of genomic information integrated with analytical tools and community-driven experiments in the fungal genomics analytical resource MycoCosm (jgi.doe.gov/fungi), which currently offers data and tools for over 500 fungal genomes, genome variation, gene expression and other functional genomics data.