Abstract
BackgroundReconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.ResultsWe compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.ConclusionA notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.Open peer reviewThis article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.
Highlights
Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes
The interest in bacteriophage biology may be at its alltime high, with the new appreciation of phage ubiquity, improved understanding of the role played by phages in controlling host abundance and in host genome evolution, and because phage genomes are the source of useful molecular reagents and new antibacterial compounds
We have reviewed the approaches to comparative genomics and taxonomy of dsDNA phages and delineated Phage Orthologous Groups (POGs), the sets of orthologous genes that are shared by three or more phages each [2]
Summary
Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Tailed bacteriophages with double-stranded DNA genomes attain the rank of the order Caudovirales and are divided into three main families according to their tail morphology: Siphoviridae (long noncontractile tail), Myoviridae (long contractile tail), and Podoviridae (short tail). Within these families, genera are defined by other molecular traits, such as the cos or pac sites, terminal redundancy and circular permutation of the genome, concatemer formation, modified bases, and the presence of DNA polymerase or RNA polymerase genes. With hundreds of bacteriophage genomes completely sequenced, it is appropriate to undertake the systematic inventory of molecular characters and to see whether it provides us with better understanding of phage evolution and with means to refine phage taxonomy
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