Genome-wide analysis of synonymous codon usage in Huaiyangshan virus and other bunyaviruses

Abstract Synonymous codon usage significantly impacts translational and transcriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has been implicated in various diseases. However, population-specific differences in codon usage biases remain largely unexplored. Here, we present a web server, https://cubap.byu.edu, to facilitate analyses of codon usage biases across populations (CUBAP). Using the 1000 Genomes Project, we calculated and visually depict population-specific differences in codon frequencies, codon aversion, identical codon pairing, co-tRNA codon pairing, ramp sequences, and nucleotide composition in 17,634 genes. We found that codon pairing significantly differs between populations in 35.8% of genes, allowing us to successfully predict the place of origin for African and East Asian individuals with 98.8% and 100% accuracy, respectively. We also used CUBAP to identify a significant bias toward decreased CTG pairing in the immunity related GTPase M (IRGM) gene in East Asian and African populations, which may contribute to the decreased association of rs10065172 with Crohn's disease in those populations. CUBAP facilitates in-depth gene-specific and codon-specific visualization that will aid in analyzing candidate genes identified in genome-wide association studies, identifying functional implications of synonymous variants, predicting population-specific impacts of synonymous variants and categorizing genetic biases unique to certain populations.

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Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic.

10.1101/2021.12.17.472912 ◽

2021 ◽

Author(s):

Ezequiel G. Mogro ◽

Daniela Bottero ◽

Mauricio J. Lozano

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Bioinformatic Analysis ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Genome Wide ◽

Life Threatening ◽

Effective Number Of Codons ◽

Over Time

SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.

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Quantifying shifts in natural selection on codon usage between protein regions: A population genetics approach

10.1101/2020.12.18.423529 ◽

2020 ◽

Author(s):

Alexander L. Cope ◽

Michael A. Gilchrist

Keyword(s):

Population Genetics ◽

Natural Selection ◽

Protein Structure ◽

Codon Usage ◽

Synonymous Codon ◽

Empirical Studies ◽

Protein Structures ◽

Synonymous Codon Usage ◽

Genome Wide ◽

Computational Analyses

AbstractEmpirical studies indicate changes to synonymous codon usage can impact protein folding. However, genome-wide computational analyses attempting to establish a more general relationship between codon usage and protein structure have often led to contradictory results. Using a population genetics model, we quantified codon-specific shifts in natural selection across and within protein structures, revealing a complex relationship between codon usage and protein structure. However, these shifts are small, suggesting differences in selection related to protein structure are either very weak or apply to relatively few codons. Using a previously published result, we demonstrate how tests for selection on codon usage can be confounded when failing to account for amino acid biases and gene expression. This work demonstrates the value of using population genetics-based models to quantify and tests for shifts in selection on codon usage. Extensions to this approach are discussed.

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Synonymous codon usage preferences in HCSV A13 strain flores

2012 IEEE-EMBS Conference on Biomedical Engineering and Sciences ◽

10.1109/iecbes.2012.6498028 ◽

2012 ◽

Author(s):

Sim-Hui Tee ◽

Sin-Liang Lim

Keyword(s):

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage

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Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns

Genomics ◽

10.1016/j.ygeno.2021.05.008 ◽

2021 ◽

Author(s):

Jayanta Kumar Das ◽

Swarup Roy

Keyword(s):

Comparative Analysis ◽

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Nucleotide Variability ◽

Usage Patterns ◽

Human Coronaviruses

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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

Genetics ◽

10.1093/genetics/159.3.1191 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1191-1199

Author(s):

Araxi O Urrutia ◽

Laurence D Hurst

Keyword(s):

Codon Usage ◽

Codon Bias ◽

Synonymous Codon ◽

Nucleotide Composition ◽

Synonymous Codon Usage ◽

Synonymous Substitutions ◽

Numerous Species ◽

Nucleotide Content ◽

Expression Breadth ◽

Human Genes

Abstract In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In contrast, in mammals, while nonequal use of alternative codons is observed, the bias is attributed to the background variance in nucleotide concentrations, reflected in the similar nucleotide composition of flanking noncoding and exonic third sites. However, a systematic examination of the covariants of codon usage controlling for background nucleotide content has yet to be performed. Here we present a new method to measure codon bias that corrects for background nucleotide content and apply this to 2396 human genes. Nearly all (99%) exhibit a higher amount of codon bias than expected by chance. The patterns associated with selectively driven codon bias are weakly recovered: Broadly expressed genes have a higher level of bias than do tissue-specific genes, the bias is higher for genes with lower rates of synonymous substitutions, and certain codons are repeatedly preferred. However, while these patterns are suggestive, the first two patterns appear to be methodological artifacts. The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans.

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Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Biochemical Genetics ◽

10.1007/s10528-021-10037-y ◽

2021 ◽

Author(s):

Xianglong Yu ◽

Jianxin Liu ◽

Huizi Li ◽

Boyang Liu ◽

Bingqian Zhao ◽

...

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Comprehensive Analysis ◽

E2 Gene ◽

Complete Genomes ◽

Synonymous Codon Usage Bias

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Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽

10.1186/s12864-021-07559-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Giovanni Franzo ◽

Claudia Maria Tucciarone ◽

Matteo Legnardi ◽

Mattia Cecchinato

Keyword(s):

Codon Usage ◽

Codon Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Accessory Proteins ◽

Effective Number ◽

Genome Composition ◽

Infectious Bronchitis ◽

Selective Forces ◽

Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. 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. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. 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. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

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