BACKGROUND: The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. RESULTS: We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes. CONCLUSION: The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.

Article Free Access Share on Genome analysis using clusters of orthologous groups (COGs) Authors: Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MDView Profile , Roman L. Tatusov National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MDView Profile , Michael Y. Galperin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MDView Profile , Michael N. Rosanov National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MDView Profile Authors Info & Claims RECOMB '98: Proceedings of the second annual international conference on Computational molecular biologyMarch 1998 Pages 135–139https://doi.org/10.1145/279069.279106Published:01 March 1998Publication History 1citation518DownloadsMetricsTotal Citations1Total Downloads518Last 12 Months27Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF

Roman L. Tatusov, Eugene V. Koonin; A simple tool to search for sequence motifs that are conserved in BLAST outputs, Bioinformatics, Volume 10, Issue 4, 1 July