In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
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Background: 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 Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. Results: We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana 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 dN/dS), 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). Conclusions: Our results indicate that while the A. thaliana 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 A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.
Mary J. O'Connell is with Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Dublin 9, Ireland -- Aisling > Doyle, Mark T.A. Donoghue, Channa Keshavaiah, and Charles Spillance are with the Genetics and Biotechnology Lab, Department of Biochemistry, Lee Maltings 2.10, University College Cork (UCC), Cork, Ireland -- Thomas E. Juenger is with the Section of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA -- Mark T.A. Donoghue, Channa Keshavaiah, Reetu Tuteja, and Charles Spillance are with the Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre, Aras de Brun C306, National University of Ireland Galway (NUIG), Galway, Ireland