title: 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 proofreading 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 C+G 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 U+A content. These suppressions are coupled with over-representation of the complementary pair of dinucleotides, CpA and UpG. In addition, we highlight the fact that odds ratios for dinucleotides are not independent variables, a situation apparently not widely appreciated in the literature. This led us to view the over-representation of CpA and UpG as a consequential outcome of UpA and CpG suppression in the virus genomes. Potential factors influencing these disturbances are discussed. In addition, higher than random incidence was observed for 'out-of-frame' stop codons in the viral RNA genomes, with some preferences for individual codons being exhibited by certain virus groups. The UAG codon appeared more common in the +1 frame, the UGA in the -1 frame.
authors.affiliation: School of Biology and Biochemistry, The Queen's University of Belfast, UK. b.rima@qub.ac.uk
authors.forename: B K
authors.initials: BK
authors.lastname: Rima
authors.forename: N V
authors.initials: NV
authors.lastname: McFerran
mesh_terms: D001483:Base Sequence; D018388:Codon, Terminator; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D012328:RNA Viruses / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D017421:Sequence Analysis
chemical_list: D018388:Codon, Terminator; D012367:RNA, Viral