title: Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members.
abstract: Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G+C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.
authors.affiliation: Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Itakura
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Saeki
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Omori
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yokoyama
authors.forename: Takakazu
authors.initials: T
authors.lastname: Kaneko
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.forename: Takuji
authors.initials: T
authors.lastname: Ohwada
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Tajima
authors.forename: Toshiki
authors.initials: T
authors.lastname: Uchiumi
authors.forename: Keina
authors.initials: K
authors.lastname: Honnma
authors.forename: Konosuke
authors.initials: K
authors.lastname: Fujita
authors.forename: Hiroyoshi
authors.initials: H
authors.lastname: Iwata
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Saeki
authors.forename: Yoshino
authors.initials: Y
authors.lastname: Hara
authors.forename: Seishi
authors.initials: S
authors.lastname: Ikeda
authors.forename: Shima
authors.initials: S
authors.lastname: Eda
authors.forename: Hisayuki
authors.initials: H
authors.lastname: Mitsui
authors.forename: Kiwamu
authors.initials: K
authors.lastname: Minamisawa
mesh_terms: D015373:Bacterial Typing Techniques; D001482:Base Composition; D041841:Bradyrhizobiaceae / Q000235:genetics / Q000502:physiology*; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D044404:Genomic Islands; D005838:Genotype; D046228:Microarray Analysis; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000382:microbiology; D013559:Symbiosis
chemical_list: D004269:DNA, Bacterial; D021903:DNA, Ribosomal Spacer