Dinucleotide and stop codon frequencies in single-stranded RNA viruses

Abstract

To identify potential selection pressures which lead to RNA sequence conservation, we examined the occurrence rates of dinucleotides in 64 single-stranded RNA virus genomes. These viruses may offer a particular insight into these pressures since their RNA-dependent RNA polymerases lack proof-reading capability. This potentiates introduction of mutations into their genomes, yet unidentified selection processes conserve the genomes to a large degree. We report a strong inverse correlation between the CMG content and the occurrence of the CpG dinucleotide (r¯0±71) in the RNA virus genomes, in contrast to earlier reports (Karlin et al., 1994, Journal of Virology 68, 2889–2897). We also detected significant suppression of UpA, correlating inversely with genomic UMA content. These sup