title: Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia.
abstract: We report the first complete genome sequence of a beta-proteobacterial nitrogen-fixing symbiont of legumes, Cupriavidus taiwanensis LMG19424. The genome consists of two chromosomes of size 3.42 Mb and 2.50 Mb, and a large symbiotic plasmid of 0.56 Mb. The C. taiwanensis genome displays an unexpected high similarity with the genome of the saprophytic bacterium C. eutrophus H16, despite being 0.94 Mb smaller. Both organisms harbor two chromosomes with large regions of synteny interspersed by specific regions. In contrast, the two species host highly divergent plasmids, with the consequence that C. taiwanensis is symbiotically proficient and less metabolically versatile. Altogether, specific regions in C. taiwanensis compared with C. eutrophus cover 1.02 Mb and are enriched in genes associated with symbiosis or virulence in other bacteria. C. taiwanensis reveals characteristics of a minimal rhizobium, including the most compact (35-kb) symbiotic island (nod and nif) identified so far in any rhizobium. The atypical phylogenetic position of C. taiwanensis allowed insightful comparative genomics of all available rhizobium genomes. We did not find any gene that was both common and specific to all rhizobia, thus suggesting that a unique shared genetic strategy does not support symbiosis of rhizobia with legumes. Instead, phylodistribution analysis of more than 200 Sinorhizobium meliloti known symbiotic genes indicated large and complex variations of their occurrence in rhizobia and non-rhizobia. This led us to devise an in silico method to extract genes preferentially associated with rhizobia. We discuss how the novel genes we have identified may contribute to symbiotic adaptation.
authors.affiliation: Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR CNRS-INRA 2594/441, 31326 Castanet-Tolosan Cedex, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Amadou
authors.forename: Géraldine
authors.initials: G
authors.lastname: Pascal
authors.forename: Sophie
authors.initials: S
authors.lastname: Mangenot
authors.forename: Michelle
authors.initials: M
authors.lastname: Glew
authors.forename: Cyril
authors.initials: C
authors.lastname: Bontemps
authors.forename: Delphine
authors.initials: D
authors.lastname: Capela
authors.forename: Sébastien
authors.initials: S
authors.lastname: Carrère
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.forename: Carole
authors.initials: C
authors.lastname: Dossat
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lajus
authors.forename: Marta
authors.initials: M
authors.lastname: Marchetti
authors.forename: Véréna
authors.initials: V
authors.lastname: Poinsot
authors.forename: Zoé
authors.initials: Z
authors.lastname: Rouy
authors.forename: Bertrand
authors.initials: B
authors.lastname: Servin
authors.forename: Maged
authors.initials: M
authors.lastname: Saad
authors.forename: Chantal
authors.initials: C
authors.lastname: Schenowitz
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Jacques
authors.initials: J
authors.lastname: Batut
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Catherine
authors.initials: C
authors.lastname: Masson-Boivin
mesh_terms: D001483:Base Sequence; D049921:Cupriavidus / Q000145:classification / Q000235:genetics*; D007887:Fabaceae / Q000382:microbiology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation / Q000235:genetics; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics; D013559:Symbiosis / Q000235:genetics