Although the number of dsDNA tailed-bacteriophage genomes that have been completely sequenced increased to more than 300 in 2007, the extreme diversity of these phages still limits our understanding of their population structure and evolution. Nonetheless, comparison of these genome sequences has brought their highly mosaic nature and extreme diversity into sharp focus, and has lead to hypotheses for how these extremely diverse “organisms” have evolved. The strength of these evolutionary deductions rests largely on the extensive knowledge that has accumulated during the intensive study into the molecular nature of the life cycles of a few ‘model system’ phages over the past half century. In particular, advances in our understanding of how the dsDNA tailed-bacteriophage packaging motor works have aided in our understanding of why the proteins that make up this motor are the most highly conserved of all the proteins that these phage encode, while most of the other phage-encoded proteins are extremely diverse when compared among (or even within) phage types. In addition, in different but related phages, similar functions are often carried out by non-homologous proteins or proteins that have diverged beyond our ability to recognize amino acid sequence similarity.
Discovery of genes that encode phage DNA packaging motor proteins in a large fraction of the one thousand completely or nearly completely sequenced bacterial genomes has shown that many phage genomes (prophages) and parts thereof reside in these bacterial genomes. There are up to twenty prophages in some bacterial genomes. These prophages contain a significant fraction of Earth's tailed-phage gene pool, and in addition, they are often very important in their bacterial host's pathogenicity. These phage and prophage genomes remain fertile ground for attempts to deduce the nature of viral evolutionary processes, and such analyses have made it clear that these phages have enjoyed a substantial amount of horizontal exchange of genetic information throughout their long histories.
