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

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dc.creatorO'Connell, Mary J.en
dc.creatorDoyle, Aisling M.en
dc.creatorJuenger, Thomas E.en
dc.creatorDonoghue, Mark TA.en
dc.creatorKeshaviah, Channaen
dc.creatorTuteja, Reetuen
dc.creatorSpillane, Charlesen
dc.date.accessioned2014-12-15T17:09:38Zen
dc.date.available2014-12-15T17:09:38Zen
dc.date.issued2012-07-17en
dc.descriptionMary 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, Irelanden
dc.description.abstractBackground: 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.en
dc.description.catalogingnotecharles.spillane@nuigalway.ieen
dc.description.departmentIntegrative Biologyen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.description.sponsorshipen
dc.identifier.Filename1756-0500-5-359.pdfen
dc.identifier.citationO’Connell, Mary J., Aisling M. Doyle, Thomas E. Juenger, Mark TA Donoghue, Channa Keshavaiah, Reetu Tuteja, and Charles Spillane. “In Arabidopsis Thaliana Codon Volatility Scores Reflect GC3 Composition rather than Selective Pressure.” BMC Research Notes 5, no. 1 (July 17, 2012): 359. doi:10.1186/1756-0500-5-359.en
dc.identifier.doidoi:10.1186/1756-0500-5-359en
dc.identifier.urihttp://hdl.handle.net/2152/27781en
dc.language.isoEnglishen
dc.publisherBMC Research Notesen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.biomedcentral.com. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectArabidopsis thalianaen
dc.subjectGC3 compositionen
dc.subjectselective pressureen
dc.subjectcodon usageen
dc.subjectmutational biasesen
dc.subjectgene expression levelsen
dc.subjectcodon volatilityen
dc.titleIn Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressureen
dc.typeArticleen

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