title: The genome of Rhizobium leguminosarum has recognizable core and accessory components.
abstract: BACKGROUND
  Rhizobium leguminosarum is an alpha-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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biology, University of York, York, UK. jpy1@york.ac.uk.
authors.forename: J Peter W
authors.initials: JP
authors.lastname: Young
authors.forename: Lisa C
authors.initials: LC
authors.lastname: Crossman
authors.forename: Andrew W B
authors.initials: AW
authors.lastname: Johnston
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Zara F
authors.initials: ZF
authors.lastname: Ghazoui
authors.forename: Katherine H
authors.initials: KH
authors.lastname: Hull
authors.forename: Margaret
authors.initials: M
authors.lastname: Wexler
authors.forename: Andrew R J
authors.initials: AR
authors.lastname: Curson
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Todd
authors.forename: Philip S
authors.initials: PS
authors.lastname: Poole
authors.forename: Tim H
authors.initials: TH
authors.lastname: Mauchline
authors.forename: Alison K
authors.initials: AK
authors.lastname: East
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Carol
authors.initials: C
authors.lastname: Churcher
authors.forename: Claire
authors.initials: C
authors.lastname: Arrowsmith
authors.forename: Inna
authors.initials: I
authors.lastname: Cherevach
authors.forename: Tracey
authors.initials: T
authors.lastname: Chillingworth
authors.forename: Kay
authors.initials: K
authors.lastname: Clarke
authors.forename: Ann
authors.initials: A
authors.lastname: Cronin
authors.forename: Paul
authors.initials: P
authors.lastname: Davis
authors.forename: Audrey
authors.initials: A
authors.lastname: Fraser
authors.forename: Zahra
authors.initials: Z
authors.lastname: Hance
authors.forename: Heidi
authors.initials: H
authors.lastname: Hauser
authors.forename: Kay
authors.initials: K
authors.lastname: Jagels
authors.forename: Sharon
authors.initials: S
authors.lastname: Moule
authors.forename: Karen
authors.initials: K
authors.lastname: Mungall
authors.forename: Halina
authors.initials: H
authors.lastname: Norbertczak
authors.forename: Ester
authors.initials: E
authors.lastname: Rabbinowitsch
authors.forename: Mandy
authors.initials: M
authors.lastname: Sanders
authors.forename: Mark
authors.initials: M
authors.lastname: Simmonds
authors.forename: Sally
authors.initials: S
authors.lastname: Whitehead
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism; D000222:Adaptation, Physiological; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001482:Base Composition; D001483:Base Sequence; D004261:DNA Replication / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D019143:Evolution, Molecular; D007887:Fabaceae / Q000382:microbiology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D009586:Nitrogen Fixation / Q000235:genetics; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D012093:Replicon; D016961:Rhizobium leguminosarum / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D013559:Symbiosis / Q000235:genetics / Q000502:physiology
chemical_list: D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D004269:DNA, Bacterial