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Rapid divergence of codon usage patterns within the rice genome

Title:

Rapid divergence of codon usage patterns within the rice genome

Wang, Huai-Chun and Hickey, Donal A. (2007) Rapid divergence of codon usage patterns within the rice genome. BMC Evolutionary Biology, 7 (Suppl ). S6. ISSN 14712148

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Official URL: http://dx.doi.org/10.1186/1471-2148-7-S1-S6

Abstract

Background
Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patterns reflect the effects of positive Darwinian selection acting at the level of translational efficiency or whether these patterns are due simply to the effects of mutational bias. In this study, we have included both intra-genomic and inter-genomic comparisons of codon usage. This allows us to distinguish more efficiently between the effects of nucleotide bias and translational selection.

Results
We show that there is an extreme degree of heterogeneity in codon usage patterns within the rice genome, and that this heterogeneity is highly correlated with differences in nucleotide content (particularly GC content) between the genes. In contrast to the situation observed within the rice genome, Arabidopsis genes show relatively little variation in both codon usage and nucleotide content. By exploiting a combination of intra-genomic and inter-genomic comparisons, we provide evidence that the differences in codon usage among the rice genes reflect a relatively rapid evolutionary increase in the GC content of some rice genes. We also noted that the degree of codon bias was negatively correlated with gene length.

Conclusion
Our results show that mutational bias can cause a dramatic evolutionary divergence in codon usage patterns within a period of approximately two hundred million years.

The heterogeneity of codon usage patterns within the rice genome can be explained by a balance between genome-wide mutational biases and negative selection against these biased mutations. The strength of the negative selection is proportional to the length of the coding sequences. Our results indicate that the large variations in synonymous codon usage are not related to selection acting on the translational efficiency of synonymous codons.

Divisions:Concordia University > Faculty of Arts and Science > Biology
Item Type:Article
Refereed:Yes
Authors:Wang, Huai-Chun and Hickey, Donal A.
Journal or Publication:BMC Evolutionary Biology
Date:08 February 2007
ID Code:7590
Deposited By:DANIELLE DENNIE
Deposited On:11 May 2011 18:10
Last Modified:11 May 2011 18:10
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