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Nonneutral GC3 and retroelement codon mimicry in Phytophthora
Rays H Y Jiang1, Francine Govers
1Laboratory of Phytopathology, Plant Sciences Group, and Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, NL-6709 PD, Wageningen, The Netherlands.
Journal of Molecular Evolution
|September 7, 2006
Summary
Phytophthora pathogens exhibit high GC3 codon bias, driven by translation efficiency selection. This codon bias is also found in their retrotransposons, suggesting selection favors mimicry for propagation.
Area of Science:
- Genomics
- Molecular Biology
- Plant Pathology
Background:
- Phytophthora are destructive eukaryotic plant pathogens.
- Phytophthora possess a unique codon usage bias, favoring GC3.
- High GC3 content can distinguish coding from noncoding genomic regions.
Purpose of the Study:
- Investigate the drivers of codon bias in Phytophthora.
- Analyze the role of selection and mutation in GC3 bias.
- Examine codon bias in Phytophthora retrotransposons and its implications.
Main Methods:
- Comparative genomics analysis across Phytophthora species.
- Assessment of gene expression levels and GC3 content.
- Identification and analysis of retrotransposon sequences and their GC content.
Main Results:
- Both selective pressure and mutation bias contribute to Phytophthora codon bias.
- Highly expressed genes show higher GC3, indicating selection for translation efficiency.
- Widespread retrotransposons in Phytophthora exhibit high GC3, mimicking host codon bias.
Conclusions:
- Translation efficiency-driven selection is the primary driver of high GC3 in Phytophthora.
- Retrotransposon codon bias mimicry suggests adaptive evolution for propagation.
- Understanding codon bias aids in differentiating genomic regions and studying pathogen evolution.
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