codon usage bias
Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes
... in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, ...
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Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda
... Reduced codon bias in the D. miranda lineage: In contrast to the striking difference between the neo-X and neo-Y in patterns of protein evolution, unpreferred synonymous substitutions do not accumulate ...
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Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in Drosophila melanogaster
... The genetic code is degenerate, such that most amino acids are encoded by more than one synonymous codon. In a wide variety of organisms, the frequencies with which such syn- onymous codons occur are nonrandom, ...
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Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection
... generally, codon usage bias, after correc- tion for background nucleotide content, covaries with any expression ...that codon usage affects ...
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Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias
... virus-like codon bias ...The codon usage bias ob- served from each segment-specific data set was compared to that observed from the corresponding counterpart ...segment-specific ...
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Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K 12 genome
... of codon usage bias ...on codon usage is used to classify ...between codon bias and expression levels for group 3 genes, ...low codon adaptation index (CAI) values ...
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Genome wide analysis of codon usage bias in Bovine Coronavirus
... of codon usage bias in BCoV, the ENC ’ s values were calculated for the complete genome of all BCoV ...third codon pos- ition) was constructed. An ENC-GC3S plot of genes whose codon ...
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How Codon Usage Bias Affects Our Ability to Recover the Tree of Life
... All domains of life tRNA are recharged with amino acids for identical codon translation when identical codons are in close proximity to each other. Recharging allows the tRNA to stay attached to the ribosome and ...
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Maximizing Transcription Efficiency Causes Codon Usage Bias
... It is much more difficult to distinguish THCU from the mutation hypothesis regarding the differences in codon usage among mammalian species of different metabolic rate[r] ...
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Codon usage bias and base composition of nuclear genes in Drosophila.
... Under the assumption that the rates and patterns of mutation in introns are the same as those of synonymous sites in the coding regions, we conclude that the variation in[r] ...
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Large-Scale Synonymous Substitutions in Cucumber Mosaic Virus RNA 3 Facilitate Amino Acid Mutations in the Coat Protein
... the codon usage bias of the coding gene. Importantly, the codon adaptation index of four chimeric mutants against dicots was similar to that of the wild-type CP gene (Table 1), indicating that ...
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In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
... [12]. Codon volatility measures the different number of mutations required for synonymous codons to be trans- formed into codons encoding a different amino acid and was proposed to reflect the selective pressure ...
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Codon Usage in Hemoglobin Coding Genes
... fact, codon usage bias has would reveal many mechanism in biology [11-13] and affect by many factors ...the codon usage in hemoglobin coding genes is studied via the CodonW, and the ...
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Synonymous Codon Usage in Bacteria
... on codon usage bias from that of maximizing translational efficiency, because highly expressed proteins are also more ...of codon usage bias reflect the intensity of selection at ...
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Solving the riddle of codon usage preferences: a test for translational selection
... Since genome size and genomic tRNA number are highly correlated (R = 0.85), it seems logical to think that both factors co-evolve in a concerted way. The evolution of genome size has largely been related to the evolution ...
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A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage
... on codon usage, with families favouring codons that are adapted to the host translational ...stronger codon usage ...their codon usage, which is shown to act via translational ...
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Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis
... The relative rate of evolution for sex-biased genes has often been used as a mea- sure of the strength of sex-specific selection. In contrast to studies in a wide variety of animals, far less is known about the molecular ...
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Coupling Between Protein Level Selection and Codon Usage Optimization in the Evolution of Bacteria and Archaea
... and selection on codon usage. The strength of the coupling between the protein level selection and codon usage bias showed a strong positive correlation with the genomic GC content. ...
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In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure
... mutational bias has played a significant role in the variation in codon usage between genomes and genes in ...of codon usage have been observed between ...of codon usage ...
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Molecular evolution in nonrecombining regions of the Drosophila melanogaster genome
... lower codon usage bias, lower GC content in coding and noncoding regions, and longer ...on codon usage persist in all heterochromatic ...
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