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. 2019 Jun 27:2019:5857285.
doi: 10.1155/2019/5857285. eCollection 2019.

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Huipeng Yao  1 , Mengyu Chen  1 , Zizhong Tang  1
Affiliations

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Huipeng Yao et al. Biomed Res Int. .

Abstract

Background: Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses.

Results: The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others).

Conclusions: All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

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Figures

Figure 1
Figure 1
ENC-GC3s plots. ENC plotted against GC3S. The red dotted line represents the expected curve derived from positions of strains when the codon usage was only determined by the GC3S composition.
Figure 2
Figure 2
The optimal codons analysis. Analysis of relative synonymous codon usage in 65 Flaviviridae viruses. (a), (b), and (c) show the RSCU values of each optimal codon.
Figure 3
Figure 3
CoA on the RSCU values. Correspondence analysis of the synonymous codon usage in Flaviviridae virus. The analysis was based on the RSCU value of the 59 synonymous codons. The positions of each virus were described in the first two main-dimensional coordinates.
Figure 4
Figure 4
Neutrality plot analysis. Neutrality plot analysis of thr 65 Flaviviridae viruses. Neutrality plot analysis of the average GC content in the first and second position of the codons and the GC content in the third position.
Figure 5
Figure 5
Phylogenetic analysis. Neighbor-joining analysis of Flaviviridae virus according to the phylogenetic analysis. Effective number of codons and GC3S content for each species are also displayed.
See this image and copyright information in PMC

References

    1. Archetti M. Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code. Journal of Molecular Evolution. 2004;59(2):258–266. doi: 10.1007/s00239-004-2620-0. - DOI - PubMed
    1. Sharp P. M., Tuohy T. M. F., Mosurski K. R. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research. 1986;14(13):5125–5143. doi: 10.1093/nar/14.13.5125. - DOI - PMC - PubMed
    1. Lesnik T., Solomovici J., Deana A., Ehrlich R., Reiss C. Ribosome traffic in E. coli and regulation of gene expression. Journal of Theoretical Biology. 2000;202(2):175–185. doi: 10.1006/jtbi.1999.1047. - DOI - PubMed
    1. Szuhan K., Yingray L., Chingyen L., et al. Dengue virus-induced ER stress is required for autophagy activation, viral replication, and pathogenesis both in vitro and in vivo. Scientific Reports. 2018;8(1) - PMC - PubMed
    1. Edgar L. R., Salazar M. I., Lopez M. J., Juan S., Alejandro S. V., Xianwu G. Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence. Biomed Research International. 2014;2014:9. doi: 10.1155/2014/851425.851425 - DOI - PMC - PubMed