Candidate Ortholog Clusters in Human, Mouse and Chicken genomes

The recently completed chicken genome, and previously available human and mouse genomes provide us an opportunity to understand the evolutionary relationship between mammals and aves at the molecular level by finding groups of orthologs in these genomes. Using a recently developed tool for automatic large scale screening of candidate orthologs in a multi-genome data, we extracted candidate ortholog clusters in these complete genomes. We obtained 14,254 candidate ortholog clusters that cover 81% of all genes in the three complete genomes. There are 9,733 candidate ortholog clusters that contain genes from all the three organisms. They cover about 70% of all genes in these organisms. Based on the Pfam annotations of genes we found that 95% of clusters are consistently annotated, since genes within each of these clusters are annotated by a single Pfam annotation. A comparison with manually curated 565 known ortholog triplets in these genomes shows that candidate ortholog clusters related to these ortholog triplets are the extensions of the ortholog triplets. Among the 565 known ortholog triplets, 549 were preserved in our results, demonstrating that our procedure was able to capture the essence of stringent criteria used by experts. Additionally, we were able to estimate the stability of the ortholog triplets and found that 562 of these are stable.