TOGs vs COGs: a Database of Supergenomes Built from Proteome Complements

Evolutionary forces acting on genomes result in gene duplications, gene losses, and gene acquisitions. Generally, it is difficult to reconstruct the exact history of the evolutionary process because of its complex nature. A widely used approach is to find orthologous groups by comparing completely sequenced genomes. This approach resulted in several databases that helped predict protein functions and provided deep insights into protein evolution. These procedures, however, did not take into account the taxonomy of organisms. Here we present a robust procedure that creates clusters of orthologous groups at each node of the evolutionary tree. As a result of this procedure, a tree of orthologous genes (TOG) is obtained. Each cluster is a “supergene” and is represented by a “consensus” sequence obtained by multiple alignment of orthologous and paralogous genes from one TOG. The procedure has been applied to the tree corresponding to the Bacillus group of bacteria. Protein complements from 26 bacterial species were used to create TOGs at all tree nodes of the tree 5 levels deep. 2520 TOGs were obtained at the root node. The analysis of these TOGs showed that they agree well with COGs from the COG database.