title: Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.
abstract: BACKGROUND
  Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics.
  
  
  RESULTS
  YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.
authors.affiliation: Inserm E0364--Université de Lille II, Faculté de Médecine Henri Warembourg, Institut Pasteur de Lille 1 rue du Pr Calmette, F-59021 Lille, France.
authors.forename: F
authors.initials: F
authors.lastname: Collyn
authors.forename: L
authors.initials: L
authors.lastname: Guy
authors.forename: M
authors.initials: M
authors.lastname: Marceau
authors.forename: M
authors.initials: M
authors.lastname: Simonet
authors.forename: C-A H
authors.initials: CA
authors.lastname: Roten
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial; D044404:Genomic Islands / Q000235:genetics*; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D037521:Virulence Factors / Q000235:genetics*; D015007:Yersinia / Q000235:genetics*
chemical_list: D009711:Nucleotides; D037521:Virulence Factors