title: Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants.
abstract: BACKGROUND
  The phenotypic consequences of large genomic architecture modifications within a clonal bacterial population are rarely evaluated because of the difficulties associated with using molecular approaches in a mixed population. Bacterial variants frequently arise among Photorhabdus luminescens, a nematode-symbiotic and insect-pathogenic bacterium. We therefore studied genome plasticity within Photorhabdus variants.
  
  
  RESULTS
  We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications.
  
  
  CONCLUSIONS
  Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolution.
authors.affiliation: INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France. sgaudriault@univ-montp2.fr
authors.forename: Sophie
authors.initials: S
authors.lastname: Gaudriault
authors.forename: Sylvie
authors.initials: S
authors.lastname: Pages
authors.forename: Anne
authors.initials: A
authors.lastname: Lanois
authors.forename: Christine
authors.initials: C
authors.lastname: Laroui
authors.forename: Corinne
authors.initials: C
authors.lastname: Teyssier
authors.forename: Estelle
authors.initials: E
authors.lastname: Jumas-Bilak
authors.forename: Alain
authors.initials: A
authors.lastname: Givaudan
mesh_terms: D000818:Animals; D005784:Gene Amplification; D017353:Gene Deletion; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D010641:Phenotype; D020637:Photorhabdus / Q000235:genetics* / Q000472:pathogenicity; D011995:Recombination, Genetic; D017172:Rhabditoidea / Q000382:microbiology; D014774:Virulence