The genome of Rhizobium leguminosarum has recognizable core and accessory components.
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.
Young
J Peter W
JP
Department of Biology, University of York, York, UK. jpy1@york.ac.uk.
Crossman
Lisa C
LC
Johnston
Andrew W B
AW
Thomson
Nicholas R
NR
Ghazoui
Zara F
ZF
Hull
Katherine H
KH
Wexler
Margaret
M
Curson
Andrew R J
AR
Todd
Jonathan D
JD
Poole
Philip S
PS
Mauchline
Tim H
TH
East
Alison K
AK
Quail
Michael A
MA
Churcher
Carol
C
Arrowsmith
Claire
C
Cherevach
Inna
I
Chillingworth
Tracey
T
Clarke
Kay
K
Cronin
Ann
A
Davis
Paul
P
Fraser
Audrey
A
Hance
Zahra
Z
Hauser
Heidi
H
Jagels
Kay
K
Moule
Sharon
S
Mungall
Karen
K
Norbertczak
Halina
H
Rabbinowitsch
Ester
E
Sanders
Mandy
M
Simmonds
Mark
M
Whitehead
Sally
S
Parkhill
Julian
J
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
D018528:ATP-Binding Cassette Transporters; D001426:Bacterial Proteins; D004269:DNA, Bacterial