Elsevier

Research in Microbiology

Volume 162, Issue 8, October 2011, Pages 737-746
Research in Microbiology

A modular view of the bacteriophage genomic space: identification of host and lifestyle marker modules

https://doi.org/10.1016/j.resmic.2011.06.006Get rights and content
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Abstract

Bacteriophage genomes can be regarded as an ensemble of modules which are accessible to the whole phage population via recombination. The time spent by prophages in the bacterial host provides them with the opportunity to exchange modules with other prophages or infecting phages. Here we analyze the modular structure of a set of 457 phages and 760 prophages extracted from completely sequenced bacterial genomes using the ACLAME database and its associated tools. We identified 91 modules of proteins with similar phylogenetic profiles. Of these, 25 and 6 are associated with temperate and virulent phages, respectively; 57 are restricted to a host or small group of hosts; and 55 could be annotated with a phage function. We use the transposable phages as a study case and show how the inclusion of prophages allows us to unveil new types of genome organization (i.e. novel module combinations) and obtain insight into the host range for this particular group, highlighting the utility of prophage prediction to better characterize phage diversity.

Keywords

Bacteriophage
Functional module
Transposable phage
Prophage
Phage evolution
Phage classification

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