Genome polarity of RNA viruses reflects the different evolutionary pressures shaping codon usage
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RNA viruses are classified by their genome polarity and replication strategies. Nucleotide composition and codon usage differ among virus groups, for instance positive-sense RNA (+ssRNA) viruses have higher GC-content than the other RNA virus groups. Codon usage of +ssRNA viruses is closer to humans showing significantly higher codon adaptation index (CAI) than those of negative-sense RNA (-ssRNA), double stranded RNA (dsRNA) and retroviruses. Ambisense viruses have high CAI comparable to that of +ssRNA virus despite their lower GC content, whereas dsRNA viruses have the lowest CAI. This may provide a benefit for +ssRNA viruses as their genomes are used as mRNA. However, analyses for influence of nucleotide composition on codon usage did not show a difference between +ssRNA and –ssRNA viruses. This suggests that genome composition and hence mutational pressure remain the major pressure causing the differences in codon usage among RNA viruses with different genome types.
The work was financial supported by Siriraj Graduate Scholarship, Siriraj Graduate Research Scholarship, Thailand Research Fund through the Royal Golden Jubilee Ph.D. Program (Grant No. PHD/0030/2556) and research grant (Grant No. IRN60W0002) from Thailand Research Fund.
- 9.Knoepfel SA, Di Giallonardo F, Däumer M, Thielen A, Metzner KJ (2011) In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing. J Virol Methods 171:329–338. https://doi.org/10.1016/j.jviromet.2010.11.016 CrossRefPubMedGoogle Scholar
- 21.Bouquet J, Cherel P, Pavio N (2012) Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. Infect Genet Evol 12:1842–1853. https://doi.org/10.1016/j.meegid.2012.07.021 CrossRefPubMedGoogle Scholar