title: Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses.
abstract: BACKGROUND
  Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD) patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA.
  
  
  RESULTS
  We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based on nucleic acid type and genome size. Similarities between eukaryotic virus phylogenies based on TUD and gene content substantiate the TUD methodology.
  
  
  CONCLUSIONS
  Differences between phenotypic and TUD analysis may provide clues to virus ancestry not previously inferred. As such, TUD analysis provides a complementary approach to morphology-based systems in analysis of virus evolution.
authors.affiliation: Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. dpride@stanford.edu
authors.forename: David T
authors.initials: DT
authors.lastname: Pride
authors.forename: Trudy M
authors.initials: TM
authors.lastname: Wassenaar
authors.forename: Chandrabali
authors.initials: C
authors.lastname: Ghose
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blaser
mesh_terms: D000465:Algorithms; D000818:Animals; D001435:Bacteriophages / Q000235:genetics*; D016000:Cluster Analysis; D019143:Evolution, Molecular; D015967:Gene Expression Regulation, Viral / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D014780:Viruses / Q000235:genetics*