ArticleGenome biology and evolution2019
Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.bioRxiv : the preprint server for biology · 2026Article
- Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.Annals of medicine and surgery (2012) · 2024Article
- Dicodon-based measures for modeling gene expression.Bioinformatics (Oxford, England) · 2023Article
- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
- Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.G3 (Bethesda, Md.) · 2023Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- Codon Pattern and Compositional Constraints Determination of Genes Associated with Chronic Periodontitis.Genes · 2022Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Distinct responses to rare codons in selecteLife · 2022Article
- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Comparative study of codon usage profiles of Zingiber officinale and its associated fungal pathogens.Molecular genetics and genomics : MGG · 2021Article
- Codon usage bias and dinucleotide preference in 29 Drosophila species.G3 (Bethesda, Md.) · 2021Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- Signatures of optimal codon usage in metabolic genes inform budding yeast ecology.PLoS biology · 2021Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
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Authors and funding
2 authors.
Funding
Abstract
Codon usage patterns are affected by both mutational biases and translational selection. The frequency at which each codon is used in the genome is directly linked to the cellular concentrations of their corresponding tRNAs. Transfer RNA abundances-as well as the abundances of other potentially relevant factors, such as RNA-binding proteins-may vary across different tissues, making it possible that genes expressed in different tissues are subject to different translational selection regimes, and thus differ in their patterns of codon usage. These differences, however, are poorly understood, having been studied only in Arabidopsis, rice and human, with controversial results in human. Drosophila melanogaster is a suitable model organism to study tissue-specific codon adaptation given its large effective population size. Here, we compare 2,046 genes, each expressed specifically in one tissue of D. melanogaster. We show that genes expressed in different tissues exhibit significant differences in their patterns of codon usage, and that these differences are only partially due to differences in GC content, expression levels, or protein lengths. Remarkably, these differences are stronger when analyses are restricted to highly expressed genes. Our results strongly suggest that genes expressed in different tissues are subject to different regimes of translational selection.
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