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Codon Usage Bias: An Endless Tale
Journal of Molecular Evolution, 2021Since the genetic code is degenerate, several codons are translated to the same amino acid. Although these triplets were historically considered to be "synonymous" and therefore expected to be used at rather equal frequencies in all genomes, we now know that this is not the case. Indeed, since several coding sequences were obtained in the late '70s and
Andrés Iriarte +2 more
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Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Evolutionary Bioinformatics, 2010 We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon ...
Soohyun Lee, Changwon Kang
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Codon Usage in Trypanosomatids: The Bias of Expression
Trends in Parasitology, 2018Translation and RNA decay, two processes in which all mRNAs are engaged, are intimately related processes. Two new studies demonstrate that, in trypanosomatids, codon usage largely shapes mRNA abundance in a translation-dependent manner. The findings indicate that mRNA decay control by codon choice is an ancient and conserved mechanism.
Esteban D, Erben, Christine, Clayton
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Codon Usage Bias and tRNA Abundance in Drosophila
Journal of Molecular Evolution, 1997Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the ...
Etsuko N Moriyama +2 more
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Codon usage bias of Catharanthus roseus
China Journal of Chinese Materia Medica, 2016This study aimed to provide guidance for the heterogenous gene expression, gene prediction and species evolution by analyzing codon usage bias of Catharanthus roseus.The codon composition and usage bias of 30 437 high-confidence coding sequences from C.roseus were analyzed and the proportion of rare codons of Escherichia coli and Saccharomyces ...
Ying, Li +4 more
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Genome-wide analysis of codon usage bias in Ebolavirus
Virus Research, 2015 Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species.
Juan Cristina +2 more
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Codon usage bias in herpesvirus
Archives of Virology, 2010In this study, I present a comprehensive analysis of codon usage bias in 43 herpesviruses for which the whole genome has been sequenced. The values of the effective number of codons revealed that the majority of the herpesviruses did not have high codon bias, with the exceptions of only simplexviruses and some varicelloviruses.
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Estimate Codon Usage Bias Using Codon Usage Analyzer (CUA)
2017One amino acid is added to a growing peptide by a ribosome through reading triple nucleotides, i.e., a codon, each time. Twenty species of amino acids are often coded by 61 codons, so one amino acid can be coded by more than one codon and the codons coding the same amino acid are called synonymous. Intriguingly, synonymous codons' usage is often uneven:
Zhenguo, Zhang, Gaurav, Sablok
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An Evaluation of Measures of Synonymous Codon Usage Bias
Journal of Molecular Evolution, 1998Synonymous codons are not generally used at equal frequencies, and this trend is observed for most genes and organisms. Several methods have been proposed and used to estimate the degree of the nonrandom use of the different synonymous codons. The estimates obtained by these methods, however, show different levels of both precision and dispersion when ...
J M, Comeron, M, Aguadé
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Codon usage by chloroplast gene is bias in Hemiptelea davidii
Journal of Genetics, 2020The base composition of the chloroplast genes is of great interest because they play a highly significant role in the evolutionary development of the plants. Evaluation of the 48 chloroplast protein-coding genes of Hemiptelea davidii showed that the average GC content was about 37.32%, while at the third codon base position alone the average GC content
Huabo Liu +3 more
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