Abstract
BackgroundEvolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes.ResultsI examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species. All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U → P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4Nes = 0.720.ConclusionThe data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.
Highlights
Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency
Identification of optimal codons Optimal codons were identified for all five species based on differences in relative synonymous codon usage (ΔRSCU) between genes with high and low levels of gene expression (Figure 1)
Based on the results from the ΔRSCU analysis, I identified 25 codons from 18 different amino acids that were used to calculate the frequency of optimal codon usage in all genes of the different species (Figure 1)
Summary
Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. Evolution of synonymous codon usage is a process where natural selection is sufficiently weak (Ns ~ 1) that the outcome is influenced by both selection, mutation and genetic drift [1,2]. Synonymous changes within and between species are sufficiently common that abundant data is available for testing evolutionary hypotheses of synonymous codon usage, explaining why much attention has been directed to understanding the relative contributions of mutation, genetic drift and natural selection to the patterns of codon bias seen within and between species. The most common model of synonymous codon usage, the "major codon preference model", assumes that one or a few synonymous codons are preferentially used in genes with high codon bias [3,5]. In most cases preferred codons correspond to the most (page number not for citation purposes)
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