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Analysis of synonymous codon usage and evolution of begomoviruses
Xiao-zhong Xu1, Qing-po Liu, Long-jiang Fan
1College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China.
Journal of Zhejiang University. Science. B
|September 3, 2008
Summary
Synonymous codon usage in begomoviruses (single-stranded DNA viruses) is primarily shaped by mutation bias. Codon usage patterns differ between Old and New World begomoviruses, offering insights into their evolutionary history.
Area of Science:
- Virology
- Molecular Biology
- Evolutionary Biology
Background:
- Begomoviruses, a genus of single-stranded DNA viruses, are significant pathogens affecting major crops globally.
- Understanding viral gene expression and evolution is crucial for disease management and control.
Purpose of the Study:
- To investigate the factors influencing synonymous codon usage variation in begomoviruses.
- To analyze the codon usage patterns of specific begomovirus genes (AV1 and BV1).
- To explore the evolutionary relationships between Old and New World begomoviruses based on codon usage.
Main Methods:
- Genome sequence analysis of begomoviruses.
- Base composition analysis of viral protein-coding genes.
- Comparison of codon usage patterns between highly and lowly expressed genes.
Main Results:
- Mutation bias significantly influences synonymous codon usage in begomoviruses.
- The AV1 and BV1 genes exhibit significant codon usage bias and high expression levels.
- Fourteen translational optimal codons were identified.
- Distinct codon usage patterns were observed between Old and New World begomoviruses.
Conclusions:
- Synonymous codon usage in begomoviruses is predominantly driven by mutation bias.
- Codon usage patterns support the evolutionary hypothesis of New World bipartite begomoviruses originating from Old World bipartite viruses, which in turn evolved from Old World monopartite begomoviruses.
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