title: Symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia.
abstract: Extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (ISs) and are termed highly reiterated sequence-possessing (HRS) strains. We analyzed the genome organization of HRS strains with the focus on IS distribution and symbiosis island structure. Using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 Mb) in the HRS strains (NK5, NK6, USDA135, 2281, USDA123, and T2), whereas no plasmids were detected in the non-HRS strain USDA110. The chromosomes of the six HRS strains (9.7 to 10.7 Mb) were larger than that of USDA110 (9.1 Mb). Using MiSeq sequences of 6 HRS and 17 non-HRS strains mapped to the USDA110 genome, we found that the copy numbers of ISRj1, ISRj2, ISFK1, IS1632, ISB27, ISBj8, and IS1631 were markedly higher in HRS strains. Whole-genome sequencing showed that the HRS strain NK6 had four small plasmids (136 to 212 kb) and a large chromosome (9,780 kb). Strong colinearity was found between 7.4-Mb core regions of the NK6 and USDA110 chromosomes. USDA110 symbiosis islands corresponded mainly to five small regions (S1 to S5) within two variable regions, V1 (0.8 Mb) and V2 (1.6 Mb), of the NK6 chromosome. The USDA110 nif gene cluster (nifDKENXSBZHQW-fixBCX) was split into two regions, S2 and S3, where ISRj1-mediated rearrangement occurred between nifS and nifB. ISs were also scattered in NK6 core regions, and ISRj1 insertion often disrupted some genes important for survival and environmental responses. These results suggest that HRS strains of soybean bradyrhizobia were subjected to IS-mediated symbiosis island shuffling and core genome degradation.
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Takayuki
authors: T
authors: Iida
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Manabu
authors: M
authors: Itakura
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Mizue
authors: M
authors: Anda
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Masayuki
authors: M
authors: Sugawara
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Tsuyoshi
authors: T
authors: Isawa
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Takashi
authors: T
authors: Okubo
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Shusei
authors: S
authors: Sato
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
authors: Kaori
authors: K
authors: Chiba-Kakizaki
authors: Graduate School of Life Sciences, Tohoku University, Sendai, Japan kiwamu@ige.tohoku.ac.jp.
authors: Kiwamu
authors: K
authors: Minamisawa
mesh_terms: D020369:Bradyrhizobium / Q000235:genetics* / Q000254:growth & development*; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D016680:Genome, Bacterial; D044404:Genomic Islands; D010802:Phylogeny; D010957:Plasmids; D053204:Root Nodules, Plant / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000382:microbiology*
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial