title: Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria.
abstract: 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.
authors.affiliation: Virginia Bioinformatics Institute, Washington St., MC 0477, Blacksburg, VA 24060, USA.
authors.forename: Steven C
authors.initials: SC
authors.lastname: Slater
authors.forename: Barry S
authors.initials: BS
authors.lastname: Goldman
authors.forename: Brad
authors.initials: B
authors.lastname: Goodner
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Farrand
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Nester
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Burr
authors.forename: Lois
authors.initials: L
authors.lastname: Banta
authors.forename: Allan W
authors.initials: AW
authors.lastname: Dickerman
authors.forename: Ian
authors.initials: I
authors.lastname: Paulsen
authors.forename: Leon
authors.initials: L
authors.lastname: Otten
authors.forename: Garret
authors.initials: G
authors.lastname: Suen
authors.forename: Roy
authors.initials: R
authors.lastname: Welch
authors.forename: Nalvo F
authors.initials: NF
authors.lastname: Almeida
authors.forename: Frank
authors.initials: F
authors.lastname: Arnold
authors.forename: Oliver T
authors.initials: OT
authors.lastname: Burton
authors.forename: Zijin
authors.initials: Z
authors.lastname: Du
authors.forename: Adam
authors.initials: A
authors.lastname: Ewing
authors.forename: Eric
authors.initials: E
authors.lastname: Godsy
authors.forename: Sara
authors.initials: S
authors.lastname: Heisel
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Houmiel
authors.forename: Jinal
authors.initials: J
authors.lastname: Jhaveri
authors.forename: Jing
authors.initials: J
authors.lastname: Lu
authors.forename: Nancy M
authors.initials: NM
authors.lastname: Miller
authors.forename: Stacie
authors.initials: S
authors.lastname: Norton
authors.forename: Qiang
authors.initials: Q
authors.lastname: Chen
authors.forename: Waranyoo
authors.initials: W
authors.lastname: Phoolcharoen
authors.forename: Victoria
authors.initials: V
authors.lastname: Ohlin
authors.forename: Dan
authors.initials: D
authors.lastname: Ondrusek
authors.forename: Nicole
authors.initials: N
authors.lastname: Pride
authors.forename: Shawn L
authors.initials: SL
authors.lastname: Stricklin
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.forename: Cathy
authors.initials: C
authors.lastname: Wheeler
authors.forename: Lindsey
authors.initials: L
authors.lastname: Wilson
authors.forename: Huijun
authors.initials: H
authors.lastname: Zhu
authors.forename: Derek W
authors.initials: DW
authors.lastname: Wood
mesh_terms: 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
chemical_list: D004269:DNA, Bacterial