The genome of Rhizobium leguminosarum has recognizable core and accessory components

J Peter W Young¹ , Lisa C Crossman² , Andrew WB Johnston³ , Nicholas R Thomson² , Zara F Ghazoui¹ , Katherine H Hull¹ , Margaret Wexler³ , Andrew RJ Curson³ , Jonathan D Todd³ , Philip S Poole⁴ , Tim H Mauchline⁴ , Alison K East⁴ , Michael A Quail² , Carol Churcher² , Claire Arrowsmith² , Inna Cherevach² , Tracey Chillingworth² , Kay Clarke² , Ann Cronin² , Paul Davis² , Audrey Fraser² , Zahra Hance² , Heidi Hauser² , Kay Jagels² , Sharon Moule² , Karen Mungall² , Halina Norbertczak² , Ester Rabbinowitsch² , Mandy Sanders² , Mark Simmonds² , Sally Whitehead² and Julian Parkhill²

¹Department of Biology, University of York, York, UK

²The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

³School of Biological Sciences, University of East Anglia, Norwich, UK

⁴School of Biological Sciences, University of Reading, Reading, UK

author email corresponding author email

Genome Biology 2006, 7:R34doi:10.1186/gb-2006-7-4-r34


Published:	26 April 2006

Subject areas: Genome studies, Microbiology and parasitology

Abstract

Background

Rhizobium leguminosarum is an α-proteobacterial N₂-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.

Results

The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.

Conclusion

Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.