RETROVIRAL OLIGONUCLEOTIDE DISTRIBUTIONS CORRELATE WITH BIASED NUCLEOTIDE COMPOSITIONS OF RETROVIRUS SEQUENCES, SUGGESTING A DUPLICATIVE STEPWISE MOLECULAR EVOLUTION

A computer-assisted analysis was made of 24 complete nucleotide sequen ces selected from the vertebrate retroviruses to represent the ten vir al groups, The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The e volution of the nucleotide sequence appears to have occurred mainly th rough at least three overlapping levels of duplication: (1) The distri butions of overrepresented (3-6)-mers are consistent with the universa l rule of a trend toward TG/CT excess and with the persistence of a ce rtain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at th e level of these (3-6)-mers supports the hypothesis of a common evolut ionary origin of vertebrate retroviruses, Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolut ionary stages. (3) Most of the (3-6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeri c or oligomeric internal iterations) and seem to be at least partly th e cause of the bias observed by other researchers at the level of retr oviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications.