ArticleMolecular biology and evolution2009
Estimating translational selection in eukaryotic genomes.
Article in Molecular biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Comparative gene annotation and orthology assignments across 301 species of Drosophilidae.PLoS biology · 2026Article
- Evolution of GC-biased gene conversion by natural selection.Genetics · 2025Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Variation in the fitness impact of translationally optimal codons among animals.Genome research · 2025Article
- Predicting gene sequences with AI to study codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Remarkable Evolutionary Rate Variations Among Lineages and Among Genome Compartments in Malaria Parasites of Mammals.Molecular biology and evolution · 2024Article
- Article
- The GC-content at the 5' ends of human protein-coding genes is undergoing mutational decay.Genome biology · 2024Article
- Differentially used codons among essential genes in bacteria identified by machine learning-based analysis.Molecular genetics and genomics : MGG · 2024Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.bioRxiv : the preprint server for biology · 2024Article
- Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.Molecular biology and evolution · 2022Article
- Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.Molecular biology and evolution · 2022Article
- Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.Genome research · 2022Article
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts.RNA biology · 2021Article
- Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide.Viruses · 2021Article
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2 authors.
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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.
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