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Open Access Research article

Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage

Xuhua Xia1* and Kwok Yung Yuen2

Author Affiliations

1 Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada

2 Department of Microbiology, University of Hong Kong, Hong Kong

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BMC Genetics 2005, 6:20  doi:10.1186/1471-2156-6-20

Published: 11 April 2005

Abstract

Background

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.

Results

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%.

Conclusion

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.