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BMC Research Notes

, 5:359

First Online: 17 July 2012Received: 13 March 2012Accepted: 17 July 2012DOI: 10.1186-1756-0500-5-359

Cite this article as: O-Connell, M.J., Doyle, A.M., Juenger, T.E. et al. BMC Res Notes 2012 5: 359. doi:10.1186-1756-0500-5-359

Abstract

BackgroundSynonymous 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.

ResultsWe 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.

ConclusionsOur 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.

AbbreviationsdNNonsynonymous substitutions per nonsynonymous site

dSSynonymous substitutions per synonymous site

dN-dSRatio of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site

GCGuanine cytosine

GC3Composition of guanine and cytosine at the third codon position

AtArabidopsis thaliana

AlArabidopsis lyrata

TAIRThe arabidopsis information resource

Pprobability

DNADeoxyribonucleic acid

CDSCoding DNA sequence

KKappa

SCRSelf-incompatibility locus

MAMMethylthioalkylmalate locus

RSCURelative synonymous codon usage

TIGRThe Institute for Genomic Research The J. Craig Venter Institute

ntnucleotide

PCRPolymerase chain reaction.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-5-359 contains supplementary material, which is available to authorized users.

Mary J O-Connell, Aisling M Doyle, Thomas E Juenger contributed equally to this work.

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Author: Mary J O-Connell - Aisling M Doyle - Thomas E Juenger - Mark TA Donoghue - Channa Keshavaiah - Reetu Tuteja - Charles S

Source: https://link.springer.com/



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