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Molecular Biology and Evolution
Article . 2008 . Peer-reviewed
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Molecular Biology and Evolution
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PubMed Central
Other literature type . 2009
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Estimating Translational Selection in Eukaryotic Genomes

Authors: dos Reis, M; Wernisch, L;

Estimating Translational Selection in Eukaryotic Genomes

Abstract

Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection on codon usage has proved complicated, perhaps due to the fact that the selection coefficients involved are very small. In this work, a population genetics model is used to measure the strength of selected codon usage bias, S, in 10 eukaryotic genomes. It is shown that the strength of selection is closely linked to expression and that reliable estimates of selection coefficients can only be obtained for genes with very similar expression levels. We compare the strength of selected codon usage for orthologous genes across all 10 genomes classified according to expression categories. Fungi genomes present the largest S values (2.24-2.56), whereas multicellular invertebrate and plant genomes present more moderate values (0.61-1.91). The large mammalian genomes (human and mouse) show low S values (0.22-0.51) for the most highly expressed genes. This might not be evidence for selection in these organisms as the technique used here to estimate S does not properly account for nucleotide composition heterogeneity along such genomes. The relationship between estimated S values and empirical estimates of population size is presented here for the first time. It is shown, as theoretically expected, that population size has an important role in the operativity of translational selection.

Country
United Kingdom
Keywords

Population Density, Genome, Saccharomyces cerevisiae, bcs, Transfer, Eukaryotic Cells, Genetic, RNA, Transfer, Protein Biosynthesis, RNA, Animals, Humans, Selection, Genetic, Codon, Selection, Research Articles

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    influence
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
91
Top 10%
Top 10%
Top 10%
Green
gold