Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members
| Autor: | Manabu Itakura, Shima Eda, Toshiki Uchiumi, Takakazu Kaneko, Hirofumi Omori, Tadashi Yokoyama, Takuji Ohwada, Kiwamu Minamisawa, Kazuhiko Saeki, Yoshino Hara, Shigeyuki Tajima, Hisayuki Mitsui, Konosuke Fujita, Satoshi Tabata, Hiroyoshi Iwata, Yuichi Saeki, Seishi Ikeda, Keina Honnma |
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| Rok vydání: | 2008 |
| Předmět: |
DNA
Bacterial Genomic Islands Genotype Sequence analysis Molecular Sequence Data Genomics Microbiology Genome DNA sequencing Evolution Molecular Nitrogen Fixation DNA Ribosomal Spacer Cluster Analysis Bradyrhizobiaceae Symbiosis Phylogeny Ecology Evolution Behavior and Systematics Genetics Base Composition Comparative Genomic Hybridization biology Phylogenetic tree food and beverages Sequence Analysis DNA Microarray Analysis biology.organism_classification Bacterial Typing Techniques Soybeans Genome Bacterial Comparative genomic hybridization Bradyrhizobium japonicum |
| Zdroj: | The ISME Journal. 3:326-339 |
| ISSN: | 1751-7370 1751-7362 |
| DOI: | 10.1038/ismej.2008.88 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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