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dc.contributor.authorO'Connell, Mary J
dc.contributor.authorDoyle, Aisling M
dc.contributor.authorJuenger, Thomas E
dc.contributor.authorDonoghue, Mark TA
dc.contributor.authorKeshavaiah, Channa
dc.contributor.authorTuteja, Reetu
dc.contributor.authorSpillane, Charles
dc.date.accessioned2012-11-27T16:02:31Z
dc.date.available2012-11-27T16:02:31Z
dc.date.issued2012-07-17
dc.identifier.citationBMC Research Notes. 2012 Jul 17;5(1):359
dc.identifier.urihttp://dx.doi.org/10.1186/1756-0500-5-359
dc.identifier.urihttp://hdl.handle.net/10147/253505
dc.description.abstractAbstract 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.
dc.titleIn Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
dc.typeJournal Article
dc.language.rfc3066en
dc.rights.holderMary J O'Connell et al.; licensee BioMed Central Ltd.
dc.description.statusPeer Reviewed
dc.date.updated2012-11-19T16:10:39Z
refterms.dateFOA2018-08-08T13:20:54Z
html.description.abstractAbstract 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.


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