ArticleVirus genes2013
Selective pressure dominates the synonymous codon usage in parvoviridae.
Article in Virus genes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae.Archives of virology · 2021Article
- Detection, genetic, and codon usage bias analyses of the VP2 gene of mink bocavirus.Virus genes · 2020Article
- Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.Journal of virological methods · 2020Article
- Evolutionary changes of the novel Influenza D virus hemagglutinin-esterase fusion gene revealed by the codon usage pattern.Virulence · 2019Article
- Comprehensive codon usage analysis of porcine deltacoronavirus.Molecular phylogenetics and evolution · 2019Article
- Codon Usage in theViruses · 2019Article
- Evolutionary and genetic analysis of the VP2 gene of canine parvovirus.BMC genomics · 2017Article
- Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- 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
- Codon usage pattern in human SPANX genes.Bioinformation · 2015Article
- Characterization of the porcine epidemic diarrhea virus codon usage bias.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2014Article
- Article
- A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection.BioMed research international · 2013Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence's composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family.
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