In <it>Arabidopsis thaliana</it> codon volatility scores reflect GC3 composition rather than selective pressure

• Main Authors: O'Connell Mary J, Doyle Aisling M, Juenger Thomas E, Donoghue Mark TA, Keshavaiah Channa, Tuteja Reetu, Spillane Charles
• Format: Article
• Language: English
• Published: BMC 2012-07-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/5/359

<p>Abstract</p> <p>Background</p> <p>Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in <it>Arabidopsis thaliana</it> in relation to gene expression levels, codon volatility, mutational biases and selective pressures.</p> <p>Results</p> <p>We have performed synonymous codon usage and codon volatility analyses for all genes in the <it>A. thaliana</it> genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by <it>dN/dS</it>), nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3).</p> <p>Conclusions</p> <p>Our results indicate that while the <it>A. thaliana</it> genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in <it>A. thaliana</it> codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.</p>