The COG database: an updated version includes eukaryotes Export

@article{citeulike:320962, abstract = {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 \~{}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.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.}, address = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. tatusov@ncbi.nlm.nih.gov}, author = {Tatusov, Roman and Fedorova, Natalie and Jackson, John and Jacobs, Aviva and Kiryutin, Boris and Koonin, Eugene and Krylov, Dmitri and Mazumder, Raja and Mekhedov, Sergei and Nikolskaya, Anastasia and Rao, B. Sridhar and Smirnov, Sergei and Sverdlov, Alexander and Vasudevan, Sona and Wolf, Yuri and Yin, Jodie and Natale, Darren}, citeulike-article-id = {320962}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-4-41}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/12969510}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=12969510}, citeulike-linkout-3 = {http://www.wormbase.org/db/misc/paper?name=WBPaper00013304}, day = {11}, doi = {10.1186/1471-2105-4-41}, issn = {1471-2105}, journal = {BMC Bioinformatics}, keywords = {cog}, month = {September}, number = {1}, pages = {41+}, posted-at = {2008-02-22 22:19:36}, priority = {2}, title = {The COG database: an updated version includes eukaryotes}, url = {http://dx.doi.org/10.1186/1471-2105-4-41}, volume = {4}, year = {2003} }

TY - JOUR ID - citeulike:320962 L3 - citeulike-article-id:320962 N2 - 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 ~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.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. IS - 1 JF - BMC Bioinformatics SN - 1471-2105 AD - National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. tatusov@ncbi.nlm.nih.gov TI - The COG database: an updated version includes eukaryotes VL - 4 SP - 41 KW - cog AU - Tatusov, Roman AU - Fedorova, Natalie AU - Jackson, John AU - Jacobs, Aviva AU - Kiryutin, Boris AU - Koonin, Eugene AU - Krylov, Dmitri AU - Mazumder, Raja AU - Mekhedov, Sergei AU - Nikolskaya, Anastasia AU - Rao, Sridhar AU - Smirnov, Sergei AU - Sverdlov, Alexander AU - Vasudevan, Sona AU - Wolf, Yuri AU - Yin, Jodie AU - Natale, Darren PY - 2003/09/11/ UR - http://dx.doi.org/10.1186/1471-2105-4-41 ER -