Evolutionary history of bacteriophages with double-stranded DNA genomes
1 Stowers Institute for Medical Research, 1000 E 50th St., Kansas City, MO 64110, USA
2 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
3 Departement d'informatique, Université du Québec à Montreal, C.P.8888, suc.Centre-Ville, Montreal, QC, H3C 3P8, Canada
4 Interdisciplinary Graduate Program in Biomedical Sciences, Kansas University Medical Center, Kansas City, KS 66160, USA
5 Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
Biology Direct 2007, 2:36 doi:10.1186/1745-6150-2-36Published: 6 December 2007
Reconstruction 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.
We 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.
A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.
Open peer review
This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.