- In the present study, all IBV complete genomes were downloaded ( n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. - Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues.. - Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. - In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle.. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Infectious bronchitis virus (IBV), a member of the family Coronaviridae, genus Coronavirus, classified within the species Avian coronavirus (https://talk.ictvonline.org. - Two non-conflicting hypotheses have been proposed to justify codon bias occurrence: 1) the mutational hy- pothesis suggests that uneven codon usage is due to the underlying genome composition and therefore to forces favouring certain types of mutations [20]. - In addition to trans- lation efficiency, codon usage has been related to gene expression level, translation fidelity, appropriate protein folding and overall organism fitness . - Relative synonymous codon usage. - The E protein was the only exception, forming a separated cluster largely overlapping with the codon usage pattern of 3a and 3b proteins, which had a highly heterogeneous distribution. - The line representing the expected Nc values, which would result from GC composition being the only factor influencing the codon usage bias, has been superimposed. - 2b), which appears to involve lower constraints in their codon usage bias. - In contrast, accessory proteins exhibited a much more restricted codon usage (and therefore lower adaptation) than chicken proteins.. - amino acid sequence) and codon usage bias of these genes, a Z-score was calculated nor- malizing the observed Rho by its expectation and variance estimated performing a random sequence generation, which allowed to consistently evaluate the degree of over- or underrepresentation and its statistical significance. - Par- ticularly, the selected models generate random sequence by shuffling of synonymous codons, without affecting the codon usage bias and the protein structure. - Relative synonymous codon usage (RSCU) and effective number of codons (Nc). - This statistic, indicative of codon bias, is calculated based on the count of a particular codon, relative to the number of times that the codon would be observed as- suming a uniform synonymous codon usage. - This analysis evaluated the influence of mutational pressure and natural selection on codon usage patterns.. - CAI is a summary value (ranging from 0 to 1) that de- scribes the codon usage of a gene relative to the codon usage of a reference set of genes, defining as translation- ally optimal codons those frequently present in highly expressed genes. - percentile of the considered tissue. - RSCU: Relative synonymous codon usage. - The online version contains supplementary material available at https://doi.. - org/10.1186/s . - The line representing the expected Nc values, which would result from GC composition being the only factor influencing the codon usage bias, has been superimposed.. - doi.org/10.1016/j.meegid . - https://doi.org ch4.. - https://doi.. - org/10.1128/JVI . - https://doi.org/10.1099/jgv.0.. - https://doi.org . - https://doi.org/10.1002/. - https://doi.org/10.13 71/journal.pone.0184401.. - https://doi.org/10.1186/s . - https://doi.org/10.1371/journal.pone.0203513.. - Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons. - https://doi.org/10.1016/j.. - 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https://doi.org/10.4236/ajmb . - Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae. - https://doi.org/10.1016/j.virol . - Codon usage bias and the evolution of influenza a viruses. - Codon Usage Biases of Influenza Virus. - https://doi.org/10.1 016/j.ympev . - https://doi.org/10.1 007/s . - https://doi.org/10.1146/a nnurev.genet.32.1.185.. - https://ggplot2.tidyverse.org.. - https://doi.org/10.1007/s . - https://doi.org/10.1016/j.molimm . - org/10.1128/IAI . - https://doi.org/10.1128/IAI.00897-09.. - https://doi.org/10.3390/diseases4030026.. - org/10.4049/jimmunol . - https://doi.org/10.1093/na r/gku075.. - https://doi.org/10.1038/na ture24039.. - Causes and implications of codon usage Bias in RNA viruses. - https://doi.org/10.1371/journal.. - The extent of codon usage bias in human RNA viruses and its evolutionary origin. - https://doi.org/1 0.1016/S X.. - https://doi.org/10.1128/JVI.02381-16.. - https://doi.org/10.1093/nar/gki261.. - 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