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 orthologous genes/proteins. Here 42 quartettes of human, yeast Saccharomyces cerevisiae, nematode Caenorhabditis elegans, and fruit fly Drosophila melanogaster candidate orthologs, defined by using similarity-based highest hit criteria (Mushegian et al., 1998 Genome Res. 8: 590-598), were reconsidered according to molecular evolutionary analysis. We found that only 14 of the 42 candidate orthologous groups can be identified to have truly one-to-one orthologous relationships, whereas other groups were characterized by one (many)-to-many orthologous relationships or even more complex scenarios involving gene duplications and/or gene losses. The result could imply that the classical one-to-one orthology might be not as common as typically accepted and automated similarity-based methods should be used with caution when accurate orthology/paralogy discrimination is required.
Xie
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Shanghai Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China.
Ding
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D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D016208:Databases, Factual; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D016678:Genome; D015801:Helminth Proteins / Q000235:genetics; D006801:Humans; D019476:Insect Proteins / Q000235:genetics; D010802:Phylogeny; D011506:Proteins / Q000235:genetics*; D020543:Proteome / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics
D005656:Fungal Proteins; D015801:Helminth Proteins; D019476:Insect Proteins; D011506:Proteins; D020543:Proteome