Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage
1 Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
2 Department of Microbiology, University of Hong Kong, Hong Kong
BMC Genetics 2005, 6:20 doi:10.1186/1471-2156-6-20Published: 11 April 2005
Bacterial genomes differ dramatically in AT%. We have developed a model to show that the genomic AT% in rapidly replicating bacterial species can be used as an index of the availability of nucleotides A and T for DNA replication in cellular medium. This index is then used to (1) study the evolution and adaptation of the bacteriophage genomic AT% in response to the differential nucleotide availability of the host and (2) test the prediction that double-stranded DNA (dsDNA) phage should exhibit better adaptation than single-stranded DNA (ssDNA) phage because the rate of spontaneous deamination, which leads to C→T or C→U mutations depending on whether C is methylated or not, is about 100-fold greater in ssDNA than in dsDNA.
We retrieved 79 dsDNA phage and 27 ssDNA phage genomes together with their host genomic sequences. The dsDNA phages have their genomic AT% better adapted to the host genomic AT% than ssDNA phage. The poorer adaptation of the ssDNA phage can be partially accounted for by the C→T(U) mutations mediated by the spontaneous deamination. For ssDNA phage, the genomic A% is more strongly correlated with their host genomic AT% than the genomic T%.
A significant fraction of variation in the genomic AT% in the dsDNA phage, and that in the genomic A% and T% of the ssDNA phage, can be explained by the difference in selection and mutation between them.