ArticleBioMed research international2013
A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection.
Article in BioMed research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- Contrasting genome composition and codon usage inVirus evolution · 2026Article
- Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2023Article
- The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.Genomics & informatics · 2022Article
- Composition and Codon Usage Pattern Results in Divergence of theJournal of fungi (Basel, Switzerland) · 2022Article
- Compositional biases in RNA viruses: Causes, consequences and applications.Wiley interdisciplinary reviews. RNA · 2022Review
- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Article
- Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts.Frontiers in microbiology · 2021Article
- Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae.Bioinformation · 2020Article
- Codon usage vis-a-vis start and stop codon context analysis of three dicot species.Journal of genetics · 2018Article
- Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus.Evolutionary bioinformatics online · 2018Article
- Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites.Genome biology and evolution · 2017Article
- Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution.BMC evolutionary biology · 2015Article
- On the biased nucleotide composition of the human coronavirus RNA genome.Virus research · 2015Article
- Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection.Virusdisease · 2014Article
- Article
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Abstract
Codon usage bias patterns have been broadly explored for many viruses. However, the relative importance of mutation pressure and natural selection is still under debate. In the present study, I tried to resolve controversial issues on determining the principal factors of codon usage patterns for DNA and RNA viruses, respectively, by examining over 38000 ORFs. By utilizing variation partitioning technique, the results showed that 27% and 21% of total variation could be attributed to mutational pressure, while 5% and 6% of total variation could be explained by natural selection for DNA and RNA viruses, respectively, in codon usage patterns. Furthermore, the combined effect of mutational pressure and natural selection on influencing codon usage patterns of viruses is substantial (explaining 10% and 8% of total variation of codon usage patterns). With respect to GC variation, GC content is always negatively and significantly correlated with aromaticity. Interestingly, the signs for the significant correlations between GC, gene lengths, and hydrophobicity are completely opposite between DNA and RNA viruses, being positive for DNA viruses while being negative for RNA viruses. At last, GC12 versus G3s plot suggests that natural selection is more important than mutational pressure on influencing the GC content in the first and second codon positions.
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