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Updated: Jul 20, 2026
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The Green Monster Process for the Generation of Yeast Strains Carrying Multiple Gene Deletions
Published on: December 15, 2012
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes
Yeong-Shin Lin1, Jake K Byrnes, Jenn-Kang Hwang
1Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.
Summary
Duplicate genes in Saccharomyces cerevisiae evolve slowly due to codon-usage bias and protein conservation, not just gene conversion. These factors influence evolutionary rates after whole-genome duplication (WGD).
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Evolution
Background:
- Many duplicate genes in Saccharomyces cerevisiae, arising from whole-genome duplication (WGD), exhibit low synonymous divergence (K(S)) and high sequence similarity.
- This slow evolution has been primarily attributed to gene conversion between these duplicate genes.
Purpose of the Study:
- To investigate the underlying causes of decelerated evolution in duplicate genes post-WGD.
- To determine the relative contributions of gene conversion, codon-usage bias, and protein sequence conservation.
Main Methods:
- Comparative genomic analysis of approximately 300 WGD gene pairs across four species.
- Comparison with orthologues in non-WGD species (Kluyveromyces waltii and Saccharomyces bayanus).
- Analysis of codon-usage bias, protein sequence conservation, and mutation patterns.
Main Results:
- Codon-usage bias and protein-sequence conservation are significant drivers of decelerated evolution in duplicate genes.
- Gene conversion's effectiveness is contingent on strong codon-usage bias or protein conservation.
- Changes in mutation patterns and tDNA copy number altered codon-usage bias and K(S) divergence between species.
- Some proteins evolved rapidly before WGD radiation but showed minimal divergence post-radiation, suggesting functional conservation.
Conclusions:
- Decelerated evolution of WGD duplicates is primarily driven by codon-usage bias and protein conservation.
- Gene conversion plays a role but is dependent on these other factors.
- Functional conservation after WGD radiation also contributes to the slow divergence of duplicate genes.
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