A Castillo

A Toussaint

AL Lloyd

Alain Givaudan

Alexandra Calteau

AP Roberts

B Doublet

C Amadou

C Canchaya

C Cazalet

C Schouler

CD Herring

CE Cowles

Claudine Médigue

CR Buell

D Mazel

D Vallenet

David Roche

E De Gregorio

E Duchaud

E Maiques

E Martinez-Garcia

EPC Rocha

F Collyn

G Garriss

G Jubelin

G Lima-Mendez

G Pavlovic

G Yang

Garret Suen

GO Poinar Jr

GR Cornelis

GR Richards

GS Vernikos

H Engelberg-Kulka

H Goodrich-Blair

Heidi Goodrich-Blair

I Chouikha

J Gerrard

J Hacker

J Parkhill

JA Shapiro

JE Barrick

Jean-Claude Ogier

JJ Farmer

JO Thaler

JP Ramsay

JW Beaber

JY Gu

K Brugirard-Ricaud

K Mathee

KN Cowles

L Klasson

L Sandner

LS Frost

M Bondi

M Brochet

M Fischer-Le Saux

M Juhas

M Lescat

M Sergeant

M Touchon

M Wu

MGI Langille

MR Hurst

MW Silby

N Boemare

N Delihas

N Vodovar

NA Moran

NE Boemare

NR Thomson

NR Waterfield

P Konczy

P Latreille

P Tailliez

P Wilkinson

Patrick Tailliez

R Heermann

R Ravatn

R Van Houdt

RA Kingsley

RJ Akhurst

Robert Zumbihl

RW Hendrix

S Abby

S Baghdiguian

S Forst

S Gaudriault

S Mann

S Shrivastava

S Tumapa

BMC Genomics

Abstract
          
            Background
            Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes).
          
          
            Results
            RGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus.
          
          
            Conclusions
            This led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution.
          </jats:sec

Steve Forst

Zoé Rouy

Sophie Gaudriault

Crossref

Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-11-568?site=bmcgenomics.biomedcentral.com

Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

Abstract

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