Elucidating Conservation of Genes in Multiple Genomes Based on Graphs Configured by Bidirectional Best-Hit Relationships

Gene classification based on orthologous relations is an important problem to understand species-universal or species-specific conservation of genes in genomes associated with phenotype in species. In the present study, we proposed a classification system of genes based on configuration of networks concerning bidirectional best-hit relations (called orthologous relation group), which makes it possible to compare multiple genomes. We have applied this method to five Bacillus species (B. subtilis, B. anthracis, B. cereus, B. halodurans, andB. thuringiensis). With regards to the the five species, 4, 776 orthologous relation groups have been obtained, and those are classified into 113 isomorphic groups. An isomorphic group may contain only orthologs or a combination of orthologs and paralogs. Gene functions and the conservativeness are discussed in view of configuration of orthologous relation groups.