RT Journal
A1 Amadou, Claire
A1 Pascal, Géraldine
A1 Mangenot, Sophie
A1 Glew, Michelle
A1 Bontemps, Cyril
A1 Capela, Delphine
A1 Carrère, Sébastien
A1 Cruveiller, Stéphane
A1 Dossat, Carole
A1 Lajus, Aurélie
A1 Marchetti, Marta
A1 Poinsot, Véréna
A1 Rouy, Zoé
A1 Servin, Bertrand
A1 Saad, Maged
A1 Schenowitz, Chantal
A1 Barbe, Valérie
A1 Batut, Jacques
A1 Médigue, Claudine
A1 Masson-Boivin, Catherine
T1 Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
JF Genome Research 
JO Genome Research 
YR 2008 
FD September 01 
VO 18 
IS 9 
SP 1472 
OP 1483 
DO 10.1101/gr.076448.108 
UL http://genome.cshlp.org/content/18/9/1472.abstract 
AB We report the first complete genome sequence of a β-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.