ArticleViruses2013
Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.
Article in Viruses, 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, 37 citations in OpenAlex.
- Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics.Virus evolution · 2026Article
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- Genetic analysis of tomato brown rugose fruit virus reveals evolutionary adaptation and codon usage bias patterns.Scientific reports · 2024Article
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- Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases.Computational and structural biotechnology journal · 2022Review
- Novel Fusari- and Toti-like Viruses, with Probable Different Origins, in the Plant Pathogenic OomyceteViruses · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Biased Mutation and Selection in RNA Viruses.Molecular biology and evolution · 2021Article
- Article
- Genome-Wide Variation in Potyviruses.Frontiers in plant science · 2019Article
- Large-Scale Synonymous Substitutions in Cucumber Mosaic Virus RNA 3 Facilitate Amino Acid Mutations in the Coat Protein.Journal of virology · 2018Article
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- Tomato Spotted Wilt Virus NSs Protein Supports Infection and Systemic Movement of a Potyvirus and Is a Symptom Determinant.Viruses · 2018Article
- Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates.Virusdisease · 2017Article
- Characterization of a Sorghum mosaic virus (SrMV) isolate in China.Saudi journal of biological sciences · 2016Article
- Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China.PloS one · 2015Article
- System analysis of synonymous codon usage biases in archaeal virus genomes.Journal of theoretical biology · 2014Article
- Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.Journal of virology · 2014Article
- The evolution of codon usage in structural and non-structural viral genes: the case of Avian coronavirus and its natural host Gallus gallus.Virus research · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.
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