Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

Figure 2

Identifying one-to-one orthologs between two genomes. The foundation of comparative genomics rests upon the ability to leverage annotation in a well-annotated genome in order to make inferences about genes in an undercharacterized genome. High sequence identity exists between orthologs (yellow genes, best hits) and paralogs (red genes, nonbest hits); however, paralogs are known to diverge in function much faster than orthologs. In order to achieve high confidence genotype-phenotype relationships via comparative genomics, it is essential to differentiate between orthologs and paralogs. Although complex relationships exist between orthologs, such as many-to-many and one-to-many/many-to-one, the most reliable annotation will be derived from one-to-one orthologs. The reciprocal best hit method for identifying orthologs successfully identifies one-to-one orthologs between two genomes if and only if the orthologs are the top hits to each.