In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

Hdl Handle:
http://hdl.handle.net/10147/253505
Title:
In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
Authors:
O'Connell, Mary J; Doyle, Aisling M; Juenger, Thomas E; Donoghue, Mark TA; Keshavaiah, Channa; Tuteja, Reetu; Spillane, Charles
Citation:
BMC Research Notes. 2012 Jul 17;5(1):359
Issue Date:
17-Jul-2012
URI:
http://dx.doi.org/10.1186/1756-0500-5-359; http://hdl.handle.net/10147/253505
Abstract:
Abstract 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.
Item Type:
Journal Article

Full metadata record

DC FieldValue Language
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-
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