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Orthologs, paralogs and genome comparisons
1Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269, USA. gogarten@uconnvm.uconn.edu
Current Opinion in Genetics & Development
|December 23, 1999
Summary
Gene duplications drive protein family evolution, but horizontal gene transfer and gene conversion complicate evolutionary analyses. Delineating protein superfamilies remains challenging due to domain shuffling.
Area of Science:
- Evolutionary biology
- Molecular biology
- Bioinformatics
Background:
- Gene duplication is a primary driver of new gene families and functions.
- Homologous sequence searching and 3D structural data reveal diverse protein functions within superfamilies.
Purpose of the Study:
- To analyze the evolution of protein superfamilies and gain insights into early evolutionary processes.
- To address the complexities in superfamily delineation arising from evolutionary mechanisms.
Main Methods:
- Analysis of homologous sequences in data banks.
- Utilizing three-dimensional structural information of proteins.
- Investigating evolutionary processes like horizontal gene transfer and gene conversion.
Main Results:
- Gene duplications generate functional diversity.
- Horizontal gene transfer complicates ancestral trait inference.
- Gene conversion can mimic independent gene duplications.
- Domain shuffling (breakup and fusion) hinders automated superfamily delineation.
Conclusions:
- Understanding protein superfamily evolution requires accounting for gene duplication, horizontal transfer, and gene conversion.
- Automated delineation of superfamilies is challenging due to complex evolutionary events like domain shuffling.