The MycoCosm portal is a fungal genomics resource developed by the US Department of Energy Joint Genome Institute (JGI) to support the integration, analysis, and dissemination of fungal genome sequences and other 'omics' data. It provides interactive web-based tools for researchers to access and analyze large amounts of genomics data. MycoCosm also encourages user participation by allowing the nomination of new fungal species for sequencing and the annotation and analysis of resulting data. By filling gaps in the Fungal Tree of Life, MycoCosm helps address important problems related to energy and the environment. MycoCosm was first developed in 2004 for the white rot fungus Phanerochaete chrysosporium and has since grown to host over 250 publicly available fungal genomes. It includes flexible tools for analyzing exponentially growing genomics and other 'omics' data sets and extends user community participation to the entire genome project cycle, from species nomination through genome annotation and comparative genomics. The portal includes tools for comparative genomics, such as PhyloGroups and EcoGroups, which allow users to compare genomes based on phylogenetic or ecological relationships. MycoCosm provides a uniform genome annotation system, using the JGI Annotation Pipeline to annotate all sequenced genomes. Predicted gene models are functionally annotated using various databases and tools, and detailed annotation reports are provided for each gene. The portal also includes a genome browser for visualizing genomic features and data, such as SNPs and gene expression profiles. User participation is encouraged through the nomination of new fungal species for sequencing via the 1000 Fungal Genomes Project. This initiative aims to fill gaps in the Fungal Tree of Life by sequencing at least two genomes for each fungal family. MycoCosm also provides a Projects menu to track ongoing genome projects and integrate a full genome project cycle into the portal. Future plans include developing new interactive tools for transcriptomics, epigenomics, population genomics, and metagenomics to support data analysis and hypothesis development. MycoCosm is a powerful and customizable data exchange resource for the fungal research community.The MycoCosm portal is a fungal genomics resource developed by the US Department of Energy Joint Genome Institute (JGI) to support the integration, analysis, and dissemination of fungal genome sequences and other 'omics' data. It provides interactive web-based tools for researchers to access and analyze large amounts of genomics data. MycoCosm also encourages user participation by allowing the nomination of new fungal species for sequencing and the annotation and analysis of resulting data. By filling gaps in the Fungal Tree of Life, MycoCosm helps address important problems related to energy and the environment. MycoCosm was first developed in 2004 for the white rot fungus Phanerochaete chrysosporium and has since grown to host over 250 publicly available fungal genomes. It includes flexible tools for analyzing exponentially growing genomics and other 'omics' data sets and extends user community participation to the entire genome project cycle, from species nomination through genome annotation and comparative genomics. The portal includes tools for comparative genomics, such as PhyloGroups and EcoGroups, which allow users to compare genomes based on phylogenetic or ecological relationships. MycoCosm provides a uniform genome annotation system, using the JGI Annotation Pipeline to annotate all sequenced genomes. Predicted gene models are functionally annotated using various databases and tools, and detailed annotation reports are provided for each gene. The portal also includes a genome browser for visualizing genomic features and data, such as SNPs and gene expression profiles. User participation is encouraged through the nomination of new fungal species for sequencing via the 1000 Fungal Genomes Project. This initiative aims to fill gaps in the Fungal Tree of Life by sequencing at least two genomes for each fungal family. MycoCosm also provides a Projects menu to track ongoing genome projects and integrate a full genome project cycle into the portal. Future plans include developing new interactive tools for transcriptomics, epigenomics, population genomics, and metagenomics to support data analysis and hypothesis development. MycoCosm is a powerful and customizable data exchange resource for the fungal research community.