Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.
The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.
Slater
Steven C
SC
Virginia Bioinformatics Institute, Washington St., MC 0477, Blacksburg, VA 24060, USA.
Goldman
Barry S
BS
Goodner
Brad
B
Setubal
João C
JC
Farrand
Stephen K
SK
Nester
Eugene W
EW
Burr
Thomas J
TJ
Banta
Lois
L
Dickerman
Allan W
AW
Paulsen
Ian
I
Otten
Leon
L
Suen
Garret
G
Welch
Roy
R
Almeida
Nalvo F
NF
Arnold
Frank
F
Burton
Oliver T
OT
Du
Zijin
Z
Ewing
Adam
A
Godsy
Eric
E
Heisel
Sara
S
Houmiel
Kathryn L
KL
Jhaveri
Jinal
J
Lu
Jing
J
Miller
Nancy M
NM
Norton
Stacie
S
Chen
Qiang
Q
Phoolcharoen
Waranyoo
W
Ohlin
Victoria
V
Ondrusek
Dan
D
Pride
Nicole
N
Stricklin
Shawn L
SL
Sun
Jian
J
Wheeler
Cathy
C
Wilson
Lindsey
L
Zhu
Huijun
H
Wood
Derek W
DW
D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D023061:Gene Order; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D010802:Phylogeny; D012231:Rhizobium / Q000235:genetics*; D017422:Sequence Analysis, DNA; D026801:Synteny
D004269:DNA, Bacterial