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.