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The genome of Rhizobium leguminosarum has recognizable core and accessory components

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Author(s)

  • L C Crossman
  • A W B Johnston
  • N R Thomson
  • Z F Ghazoui
  • K H Hull
  • M Wexler
  • A R J Curson
  • J D Todd
  • P S Poole
  • T H Mauchline
  • A K East
  • M A Quail
  • C Churcher
  • C Arrowsmith
  • I Cherevach
  • T Chillingworth
  • K Clarke
  • A Cronin
  • P Davis
  • A Fraser
  • Z Hance
  • H Hauser
  • K Jagels
  • S Moule
  • K Mungall
  • H Norbertczak
  • E Rabbinowitsch
  • M Sanders
  • M Simmonds
  • S Whitehead
  • J Parkhill

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Publication details

JournalGenome biology
DatePublished - 2006
Issue number4
Volume7
Number of pages20
Pages (from-to)-
Original languageEnglish

Abstract

Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-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 overrepresented 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.

Bibliographical note

© 2006 Young et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Research areas

  • AGROBACTERIUM-TUMEFACIENS C58, SYMBIOTIC NITROGEN-FIXATION, 3 GROEL HOMOLOGS, BACTERIAL GENOMES, ESCHERICHIA-COLI, BV-VICIAE, BIOVAR VICIAE, FIELD POPULATIONS, EVOLUTIONARY IMPLICATIONS, TRANSFERRED GENES

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