Over 40 eukaryotic genomes have been annotated using JGI Annotation Pipeline, which combines several gene prediction and annotation tools. Predicted genes and annotations are accessible via interactive visualization tools integrated into JGI Genome Portal. The diverse set of annotated genomes represents the major branches of the tree of life and provides basis for comparative genomics analysis. This comparative analysis as well as analysis of available experimental data (ESTs, microarrays, proteomics) enable validation of predicted genes. In addition, community-driven manual curation of predicted genes and functions in annotated genomes further improves their quality.

We annotated over 60 eukaryotic genomes increasing annotation throughput ~;10 fold in the last 5 years with improved annotation process, automated annotation pipeline, and further developed genome analysis tools integrated in the Eukaryotic Genome Portal. We developed a Community Annotation model, unique across sequencing centers, to achieve higher quality of annotations, teach and train new users, and build stronger genome user communities. These tools will serve as a platform for programmatic approach to scaling up sequencing and analysis of microbial eukaryotic, for example, JGI Fungal Program, along the directions of (i) sequencing phylogenetic breadth, (ii) deeper sampling DOE mission relevant organisms, and (iii) exploring ecological diversity. A diverse portfolio of microbial eukaryotes (68 fungal and 21 algal projects at different stages in JGI pipeline) and DOE mission positions the JGI to sequence a broad range of microbial eukaryotes.

MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other omics data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.