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The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA - BMC Bioinformatics (2003)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. tatusov@ncbi.nlm.nih.gov

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 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.

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Phyletic patterns of KOGs. All, include representatives from each of the 7 analyzed species; All-Ec, include representatives from each of 6 species other than Encephalitozoon cuniculi; All animals, include representatives from three animal genomes only; All fungi, include representatives from two fungal genomes only.
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Figure 2: Phyletic patterns of KOGs. All, include representatives from each of the 7 analyzed species; All-Ec, include representatives from each of 6 species other than Encephalitozoon cuniculi; All animals, include representatives from three animal genomes only; All fungi, include representatives from two fungal genomes only.

Mentions: Examination of the phyletic patterns of KOGs points to the existence of a conserved eukaryotic gene core as well as substantial diversity (Fig. 2); this clearly resembles the evolutionary pattern seen previously during the analysis of archaeal COGs [41]. The genes represented in each of the 7 analyzed genomes comprise ~20% of the KOG set and approximately the same number of KOGs includes 6 species, with the exception of the microsporidian. The prevalence of the latter pattern is not surprising given that microsporidia are intracellular parasites with minimal metabolic capabilities and a dramatically reduced genome [38]. The next largest group consists of animal-specific COGs, which, again, could be expected because animals are the only lineage of complex eukaryotes that is represented by more than one species in the analyzed set of genomes. However, a notable observation is that ~30% of the KOGs had "odd" phyletic patterns, e.g., are represented in one animal, one plant and one fungal species (Fig. 2).


The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA - BMC Bioinformatics (2003)

Phyletic patterns of KOGs. All, include representatives from each of the 7 analyzed species; All-Ec, include representatives from each of 6 species other than Encephalitozoon cuniculi; All animals, include representatives from three animal genomes only; All fungi, include representatives from two fungal genomes only.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC222959&req=5

Figure 2: Phyletic patterns of KOGs. All, include representatives from each of the 7 analyzed species; All-Ec, include representatives from each of 6 species other than Encephalitozoon cuniculi; All animals, include representatives from three animal genomes only; All fungi, include representatives from two fungal genomes only.
Mentions: Examination of the phyletic patterns of KOGs points to the existence of a conserved eukaryotic gene core as well as substantial diversity (Fig. 2); this clearly resembles the evolutionary pattern seen previously during the analysis of archaeal COGs [41]. The genes represented in each of the 7 analyzed genomes comprise ~20% of the KOG set and approximately the same number of KOGs includes 6 species, with the exception of the microsporidian. The prevalence of the latter pattern is not surprising given that microsporidia are intracellular parasites with minimal metabolic capabilities and a dramatically reduced genome [38]. The next largest group consists of animal-specific COGs, which, again, could be expected because animals are the only lineage of complex eukaryotes that is represented by more than one species in the analyzed set of genomes. However, a notable observation is that ~30% of the KOGs had "odd" phyletic patterns, e.g., are represented in one animal, one plant and one fungal species (Fig. 2).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. tatusov@ncbi.nlm.nih.gov

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 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.

Show MeSH