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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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An example of a complex eukaryotic KOG: globins and related hemoproteins. The systematic protein names of the KOG members are listed under each species. To the left of the KOG proper is the similarity dendrogram produced from the BLAST scores between the KOG members. This is a crude clustering, which should not be construed as a phylogenetic tree.
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Figure 3: An example of a complex eukaryotic KOG: globins and related hemoproteins. The systematic protein names of the KOG members are listed under each species. To the left of the KOG proper is the similarity dendrogram produced from the BLAST scores between the KOG members. This is a crude clustering, which should not be construed as a phylogenetic tree.

Mentions: To illustrate the typical composition of a KOG, some of the problems that tend to emerge with their construction, and possible biological implications, we briefly discuss here KOG3378, which includes proteins already mentioned above as a typical case of paralogy and orthology, namely, the globins (Fig. 3). Globins are small (typically, between 140 and 150 amino acid residues) and relatively poorly conserved proteins. As a consequence, the initial, automatic procedure for KOG construction produced a candidate KOG consisting of only 3 proteins from 3 species: S. cerevisiae YGR234w, its ortholog from S. pombe SPAC869.02c, and human neuroglobin Hs10864065. The remaining proteins were brought into the KOG manually, as the result of examination of BLAST search outputs, focused on the conservation of the globin-specific sequence motifs. The final KOG is represented in 6 of the 7 analyzed eukaryotic species, with the sole exception of E. cuniculi (Fig. 3). The most remarkable aspect of this KOG is the apparent independent proliferation of genes for globins and globin-like proteins in vertebrates (represented here by humans): 11 paralogs, and nematodes (C. elegans): 24 paralogs (CE23430 and CE23431 are parts of the same gene). Strictly speaking, to demonstrate that these expansions are, indeed, independent, rather than ancestral, complete phylogenetic analysis is required, which is a difficult task given the low sequence conservation in many members of the KOGs. However, the presence of only one globin homolog in D. melanogaster is best compatible with hypothesis of lineage-specific expansion because, regardless of the exact topology of the animal phylogenetic tree [42], the alternative to this hypothesis would involve massive loss of globin-like genes in insects. Furthermore, this hypothesis is also compatible with the topology of the crude similarity dendrogram, which accompanies the KOG and in which the majority of human and nematode members form distinct clusters (Fig. 3). Thus, at this stage, the most likely, conservative interpretation of the evolutionary relationship between vertebrates and nematode globins is that they comprise co-orthologous sets and are legitimately included in the same KOG. Similarly, the two paralogous leghemoglobins from A. thaliana should be considered co-orthologous to the human and C. elegans paralogous sets.


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)

An example of a complex eukaryotic KOG: globins and related hemoproteins. The systematic protein names of the KOG members are listed under each species. To the left of the KOG proper is the similarity dendrogram produced from the BLAST scores between the KOG members. This is a crude clustering, which should not be construed as a phylogenetic tree.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC222959&req=5

Figure 3: An example of a complex eukaryotic KOG: globins and related hemoproteins. The systematic protein names of the KOG members are listed under each species. To the left of the KOG proper is the similarity dendrogram produced from the BLAST scores between the KOG members. This is a crude clustering, which should not be construed as a phylogenetic tree.
Mentions: To illustrate the typical composition of a KOG, some of the problems that tend to emerge with their construction, and possible biological implications, we briefly discuss here KOG3378, which includes proteins already mentioned above as a typical case of paralogy and orthology, namely, the globins (Fig. 3). Globins are small (typically, between 140 and 150 amino acid residues) and relatively poorly conserved proteins. As a consequence, the initial, automatic procedure for KOG construction produced a candidate KOG consisting of only 3 proteins from 3 species: S. cerevisiae YGR234w, its ortholog from S. pombe SPAC869.02c, and human neuroglobin Hs10864065. The remaining proteins were brought into the KOG manually, as the result of examination of BLAST search outputs, focused on the conservation of the globin-specific sequence motifs. The final KOG is represented in 6 of the 7 analyzed eukaryotic species, with the sole exception of E. cuniculi (Fig. 3). The most remarkable aspect of this KOG is the apparent independent proliferation of genes for globins and globin-like proteins in vertebrates (represented here by humans): 11 paralogs, and nematodes (C. elegans): 24 paralogs (CE23430 and CE23431 are parts of the same gene). Strictly speaking, to demonstrate that these expansions are, indeed, independent, rather than ancestral, complete phylogenetic analysis is required, which is a difficult task given the low sequence conservation in many members of the KOGs. However, the presence of only one globin homolog in D. melanogaster is best compatible with hypothesis of lineage-specific expansion because, regardless of the exact topology of the animal phylogenetic tree [42], the alternative to this hypothesis would involve massive loss of globin-like genes in insects. Furthermore, this hypothesis is also compatible with the topology of the crude similarity dendrogram, which accompanies the KOG and in which the majority of human and nematode members form distinct clusters (Fig. 3). Thus, at this stage, the most likely, conservative interpretation of the evolutionary relationship between vertebrates and nematode globins is that they comprise co-orthologous sets and are legitimately included in the same KOG. Similarly, the two paralogous leghemoglobins from A. thaliana should be considered co-orthologous to the human and C. elegans paralogous sets.

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
Related in: MedlinePlus