The COG database: an updated version includes eukaryotes

The availability of many essentially complete prokaryotic and eukaryotic genome sequences created both the demand and the opportunity for an evolutionary classification of genes based on orthologous relationships, a natural framework for comparative genomics and functional annotation. This paper describes a major update to the system for delineating Clusters of Orthologous Groups of proteins (COGs) from sequenced genomes of prokaryotes and unicellular eukaryotes, and the construction of clusters of predicted orthologs for seven eukaryotic genomes, which the authors name KOGs (eukaryotic orthologous groups).

The COG collection comprises 138,458 proteins forming 4873 COGs, about 75% of the 185,505 predicted proteins encoded in 66 unicellular genomes, while the KOG set includes 4852 clusters covering 59,838 proteins, roughly 54% of the analyzed eukaryotic gene products from species such as worm, fruit fly, human, Arabidopsis, two fungi, and a microsporidian parasite. About 20% of KOGs form a conserved core present in all analyzed species, a much larger ubiquitous fraction than in COGs, and the updated resource is expected to aid functional annotation and genome-wide evolutionary studies.