title: Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome.
abstract: Using a computational pipeline based on similarity networks reconstruction we analysed the 1133 genes of the Burkholderia vietnamiensis (Bv) G4 five plasmids, showing that gene and operon duplication played an important role in shaping the plasmid architecture. Several single/multiple duplications occurring at intra- and/or interplasmids level involving 253 paralogous genes (stand-alone, clustered or operons) were detected. An extensive gene/operon exchange between plasmids and chromosomes was also disclosed. The larger the plasmid, the higher the number and size of paralogous fragments. Many paralogs encoded mobile genetic elements and duplicated very recently, suggesting that the rearrangement of the Bv plastic genome is ongoing. Concerning the "molecular habitat" and the "taxonomical status" (the Preferential Organismal Sharing) of Bv plasmid genes, most of them have been exchanged with other plasmids of bacteria belonging (or phylogenetically very close) to Burkholderia, suggesting that taxonomical proximity of bacterial strains is a crucial issue in plasmid-mediated gene exchange.
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Isabel
authors.initials: I
authors.lastname: Maida
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlandini
authors.affiliation: Tree and Timber Institute, National Research Council, Via Madonna del Piano, 10 I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Emiliani
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Maria Cristiana
authors.initials: MC
authors.lastname: Papaleo
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Perrin
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, Via Madonna del Piano 6, University of Florence, I-50019 Sesto F.no, Firenze, Italy. Electronic address: renato.fani@unifi.it.
authors.forename: Renato
authors.initials: R
authors.lastname: Fani
mesh_terms: D019117:Burkholderia / Q000145:classification / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D015321:Gene Rearrangement; D005798:Genes, Bacterial; D009876:Operon; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial
keywords: Blast2Network; Gene duplication; Gene sharing; Molecular habitat; Molecular remodelling