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Dinucleotide and stop codon frequencies in single-stranded RNA viruses
1School of Biology and Biochemistry, The Queen's University of Belfast, UK. b.rima@qub.ac.uk
The Journal of General Virology
|November 21, 1997
Summary
RNA virus genomes show conserved sequences due to selection pressures, not just random mutation. CpG and UpA dinucleotides are suppressed, while CpA and UpG are over-represented, influencing viral RNA conservation.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- Single-stranded RNA viruses possess RNA-dependent RNA polymerases lacking proofreading, leading to high mutation rates.
- Despite high mutation rates, viral RNA genomes exhibit significant sequence conservation, suggesting underlying selection pressures.
Purpose of the Study:
- To investigate selection pressures driving RNA sequence conservation in viral genomes.
- To analyze dinucleotide frequencies and their correlation with genomic content in RNA viruses.
Main Methods:
- Analysis of dinucleotide occurrence rates in 64 single-stranded RNA virus genomes.
- Statistical correlation analysis between C+G/U+A content and specific dinucleotide frequencies.
- Examination of dinucleotide odds ratios for independence.
Main Results:
- A strong inverse correlation (r=0.71) was found between C+G content and CpG dinucleotide occurrence.
- Significant suppression of UpA dinucleotides was observed, correlating inversely with genomic U+A content.
- CpA and UpG dinucleotides were over-represented, likely as a consequence of CpG and UpA suppression.
Conclusions:
- Dinucleotide frequencies in viral RNA are not independent and are influenced by selection pressures.
- CpG and UpA suppression, coupled with CpA and UpG over-representation, contribute to RNA sequence conservation in viruses.
- Further investigation into factors influencing these observed dinucleotide patterns is warranted.