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Rapid, Seamless Generation of Recombinant Poxviruses using Host Range and Visual Selection
Published on: May 24, 2020
Genus specific evolution of codon usage and nucleotide compositional traits of poxviruses
Sourav Roychoudhury1, Archana Pan, Debaprasad Mukherjee
1School of Information Technology, Bengal Engineering and Science University, Shibpur Howrah, 711103 West Bengal, India. src_4u@yahoo.co.in
Virus Genes
|March 4, 2011
Summary
Poxviruses exhibit diverse codon usage patterns, influenced by their nucleotide composition bias, which varies significantly across genera but shows conservation within them. This suggests distinct evolutionary paths for poxviruses based on AT or GC richness.
Area of Science:
- Virology
- Molecular Biology
- Evolutionary Biology
Background:
- Poxviruses (Poxviridae family) display complex nucleotide compositional features in their coding regions.
- Codon usage patterns within Poxviridae are generally divergent across species, with some conserved traits observed at the genus level.
Purpose of the Study:
- To investigate the relationship between nucleotide composition and codon usage patterns across different genera of Poxviruses.
- To explore the evolutionary trajectories of Poxviruses concerning their nucleotide bias and codon preferences.
Main Methods:
- Analysis of nucleotide composition (AT-rich vs. GC-rich) in coding regions of various Poxvirus genera.
- Examination of codon usage patterns, including preferences for AT- or GC-ending codons.
- Application of correspondence analysis and cluster analysis to assess codon usage divergence and evolutionary relationships.
Main Results:
- Significant nucleotide compositional bias (AT-rich or GC-rich) was observed in genera like Avipoxvirus, Capripoxvirus, Orthopoxvirus, and Parapoxvirus.
- Poxviruses from AT-rich genera predominantly use AT-ending codons, while GC-rich genera favor GC-ending codons, aligning with their compositional bias.
- Gene length and expression levels also showed some influence on codon usage in specific Poxvirus genera.
- Correspondence and cluster analyses supported genus-specific evolution of Poxvirus codon usage, indicating two main evolutionary trajectories.
Conclusions:
- Poxvirus codon usage is strongly correlated with their intrinsic nucleotide composition bias, which is largely conserved within genera but divergent across them.
- Poxviruses have evolved along distinct evolutionary paths, primarily differentiated by their nucleotide composition (AT-rich vs. GC-rich) and resulting codon preferences.
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