The COG database: an updated version includes eukaryotes

By Bmc Bioinformatics, R. Tatusov, N. Fedorova, John D. Jackson, A. Jacobs, B. Kiryutin, Eugene V. Koonin, D. M. Krylov, R. Mazumder, S. Mekhedov and 8 more. 2003

4,498 citations recorded by the source corpus.

BackgroundThe 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.ResultsWe 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 euk aryotic o rthologous g roups. 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 euk aryotic o rthologous g roups (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 ~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 ~20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (~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.ConclusionThe 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.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “In addition, manually curated OGs available for the three domains of life were integrated into the corresponding levels in eggNOG, namely bacterial subset of COGs (23), archaeal arCOGs (24) and eukaryotic KOGs (25).”
The HHpred interactive server for protein homology detection and structure prediction (2005, background): “Databases: A wide range of regularly updated structure and protein family databases can be searched: the PDB (21), SCOP (22), Pfam (23), SMART (24), COG (25) and CDD (26).”
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria (2013, background): “All studied TFs were classified into 55 protein families based on their domain composition in the Pfam [36], COG [37] and Superfamily [38] libraries (see TF families classification and domains architecture in Additional file 1).”
Entrez Gene: gene-centered information at NCBI (2010, unknown): “Information about Clusters of Orthologous Groups (COGs) (5) is available via Links menus.”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “The function class assignment is based on the inclusion of the respective genes in COGs (34).”
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data (2012, methodology): “The MicroScope analysis tools and graphical interfaces are organized as several categories (main tool bar in the black rectangle): The ‘MaGe’ and ‘Genomic tools’ menus contain functionalities needed for the curation process and for the summary of the automatic and expert annotation (Genome overview,”
Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, background): “…efforts at producing and making available ortholog mappings by various means (Alexeyenko et al., 2006; Deluca et al., 2006; Fulton et al., 2006; Tatusov et al., 2003; von Mering et al., 2007), computational biologists often need their own orthologous sets for variable reasons such as: (1) a…”
Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis (2006, background): “Briefly, the gatB gene encodes aspartyl/glutamyl-tRNA amidotransferase subunit B that synthesizes charged tRNAs in organisms lacking certain tRNA synthetases; coxA encodes a catalytic subunit of cytochrome oxidase of the respiratory chain; hcpA encodes a functionally uncharacterized protein whose le”
The Proteomics Protocols Handbook (2005, background): “In addition, solubilization of Jurkat membranes with Tween-20, Brij 58, and Lubrol WX yielded significantly more solubilized protein than either Triton or CHAPS (60).”