Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

Oct 23, Tue 2007
11:00 am, MRB 200 Conference Room

Dr. Arcady Mushegian

Department of Microbiology, Molecular Genetics & Immunology, The University of Kansas School of Medicine

Director of Bioinformatics Center, Stowers Institute for Medical Research

Evolutionary history of bacteriophages with double-stranded DNA genomes

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. Thus, a notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.