The COG database: an updated version includes eukaryotes.
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.


CONCLUSIONS
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.
Tatusov
Roman L
RL
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. tatusov@ncbi.nlm.nih.gov
Fedorova
Natalie D
ND
Jackson
John D
JD
Jacobs
Aviva R
AR
Kiryutin
Boris
B
Koonin
Eugene V
EV
Krylov
Dmitri M
DM
Mazumder
Raja
R
Mekhedov
Sergei L
SL
Nikolskaya
Anastasia N
AN
Rao
B Sridhar
BS
Smirnov
Sergei
S
Sverdlov
Alexander V
AV
Vasudevan
Sona
S
Wolf
Yuri I
YI
Yin
Jodie J
JJ
Natale
Darren A
DA
D000818:Animals; D030561:Databases, Nucleic Acid / Q000639:trends; D030562:Databases, Protein / Q000639:trends*; D005057:Eukaryotic Cells / Q000737:chemistry / Q000502:physiology; D019143:Evolution, Molecular; D006801:Humans; D009316:National Institutes of Health (U.S.); D011506:Proteins / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D009626:Terminology as Topic; D014481:United States
D011506:Proteins