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Comparative Study
. 2008 Sep;18(9):1472-83.
doi: 10.1101/gr.076448.108. Epub 2008 May 19.

Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Claire Amadou  1 , Géraldine Pascal, Sophie Mangenot, Michelle Glew, Cyril Bontemps, Delphine Capela, Sébastien Carrère, Stéphane Cruveiller, Carole Dossat, Aurélie Lajus, Marta Marchetti, Véréna Poinsot, Zoé Rouy, Bertrand Servin, Maged Saad, Chantal Schenowitz, Valérie Barbe, Jacques Batut, Claudine Médigue, Catherine Masson-Boivin
Affiliations
Comparative Study

Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Claire Amadou et al. Genome Res. 2008 Sep.

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.

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Figures

Figure 1.
Figure 1.
Unrooted 16S rDNA tree of completely sequenced rhizobia and Ralstonia/Cupriavidus strains. Rhizobia are in bold. α, β, and γ represent different subdivisions of proteobacteria. The tree was constructed by using the neighbor-joining method. 16S rDNA sequences are available in GenBank. For Ralstonia/Cupriavidus species, which possess nonidentical 16S rDNA, a consensus sequence was determined with DNAstar.
Figure 2.
Figure 2.
Synteny plots between the C. taiwanensis and C. eutrophus genomes. Conserved gene clusters, i.e., synteny groups, were computed according to Vallenet et al. (2006). Synteny groups containing a minimum of five (A,B) or three (C) genes are shown for colinear regions (purple), and for inverted regions (blue). The display has been obtained using the MaGe graphical interface of the CupriaviduScope project (https://www.genoscope.cns.fr/agc/mage).
Figure 3.
Figure 3.
Circular representation of the three replicons of C. taiwanensis LMG19424. Circles, from the inside out, show: (1) GC skew; (2) tRNA and rRNA (green) and TE (pink); (3) CDS common to all Cupriavidus (green); (4) GC deviation (red when significantly different from the mean); (5) common CDS to C. taiwanensis LMG19424 and C. eutrophus H16 (purple); (6) for chromosomes 1 and 2 only, SR of C. taiwanensis versus C. eutrophus (yellow when a SR occurs at the same location in H16, red otherwise). Circles were drawn using GenVision software (http://www.dnastar.com/products/genvision.php).
Figure 4.
Figure 4.
Symbiotic features of C. taiwanensis. (A) Map of symbiotic regions. Genes are colored according to their name. (Arrows) The location of potential nod-boxes. (B) Sequence and position on pRalta of predicted nod-boxes. (C) Chemical structure of Nod factors produced by C. taiwanensis. (Arrows) Contribution of Nod proteins to NF biosynthesis based on the literature.
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