The EBP roadmap calls for sequencing and annotating ∼1.5 million known eukaryotic species in three phases over a 10-year period using a phylogenomic approach.
During the three years of Phase I, one of the most important goals is to create annotated chromosome-scale reference assemblies for at least one representative species of each of the ∼9,000 eukaryotic taxonomic families. Nucleotide divergence and divergence time will be additional factors in the selection of species so that balance across eukaryotic taxa is achieved. High-quality reference assemblies at the family level will ensure robustness of comparative genomic analyses by providing complete gene sets as well as ordered and oriented syntenic blocks created by genome scaffolding methods. In addition, these genomes will be useful for classification of extant and new species, identification of genetic changes associated with specialized traits in specific lineages, in silico reference-assisted scaffolding of assemblies produced in Phase II and Phase III of the project, in silico reconstruction of ancestral genomes, and rescue of species from extinction. A full description of the roadmap, overall strategy, and estimated costs can be found in the PNAS Perspective SI Appendix.