Investigating 42 candidate orthologous protein groups by molecular evolutionary analysis on genome scale

It is one of key problems for comparative genomics to accurately identify o rthologous genes/proteins. Here 42 quartettes of human, yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans, and fruit fly Drosophila mela nogaster candidate orthologs, defined by using similarity-based highest hit criteria (Mushegian et al., 1998 Genome Res. 8. 590-598), were reconsidere d according to molecular evolutionary analysis. We found that only 14 of th e 42 candidate orthologous groups can be identified to have truly one-to-on e orthologous relationships, whereas other groups were characterized by one (many)-to-many orthologous relationships or even more complex scenarios in volving gene duplications and/or gene losses. The result could imply that t he classical one-to-one orthology might be not as common as typically accep ted and automated similarity-based methods should be used with caution when accurate orthology/paralogy discrimination is required. (C) 2000 Elsevier Science B.V. All rights reserved.