Genome Analysis of a Novel <i>Bradyrhizobium</i> sp. DOA9 Carrying a Symbiotic Plasmid

<div><p><i>Bradyrhizobium</i> sp. DOA9 isolated from the legume <i>Aeschynomene americana</i> exhibited a broad host range and divergent nodulation (<i>nod</i>) genes compared with other members of the <i>Bradyrhizobiaceae</i>. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid of 0.7 Mbp. The chromosome showed highest similarity with that of the <i>nod</i> gene-harboring soybean symbiont <i>B. japonicum</i> USDA110, whereas the plasmid showed highest similarity with pBBta01 of the <i>nod</i> gene-lacking photosynthetic strain BTAi1, which nodulates <i>Aeschynomene</i> species. Unlike in other bradyrhizobia, the plasmid of DOA9 encodes genes related to symbiotic functions including nodulation, nitrogen fixation, and type III/IV protein secretion systems. The plasmid has also a lower GC content (60.1%) than the chromosome (64.4%). These features suggest that the plasmid could be the origin of the symbiosis island that is found in the genome of other bradyrhizobia. The <i>nod</i> genes of DOA9 exhibited low similarity with those of other strains. The <i>nif</i> gene cluster of DOA9 showed greatest similarity to those of photosynthetic bradyrhizobia. The type III/IV protein secretion systems of DOA9 are similar to those of <i>nod</i> gene-harboring <i>B. elkanii</i> and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between <i>nod</i> gene-harboring bradyrhizobia and <i>nod</i> gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the <i>Bradyrhizobiaceae</i> during ecological adaptation. <i>Bradyrhizobium</i> sp. DOA9 isolated from the legume <i>Aeschynomene americana</i> exhibited a broad host range and divergent nodulation (<i>nod</i>) genes compared with other members of the <i>Bradyrhizobiaceae</i>. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid of 0.7 Mbp. The chromosome showed highest similarity with that of the <i>nod</i> gene-harboring soybean symbiont <i>B. japonicum</i> USDA110, whereas the plasmid showed highest similarity with pBBta01 of the <i>nod</i> gene-lacking photosynthetic strain BTAi1, which nodulates <i>Aeschynomene</i> species. Unlike in other bradyrhizobia, the plasmid of DOA9 encodes genes related to symbiotic functions including nodulation, nitrogen fixation, and type III/IV protein secretion systems. The plasmid has also a lower GC content (60.1%) than the chromosome (64.4%). These features suggest that the plasmid could be the origin of the symbiosis island that is found in the genome of other bradyrhizobia. The <i>nod</i> genes of DOA9 exhibited low similarity with those of other strains. The <i>nif</i> gene cluster of DOA9 showed greatest similarity to those of photosynthetic bradyrhizobia. The type III/IV protein secretion systems of DOA9 are similar to those of <i>nod</i> gene-harboring <i>B. elkanii</i> and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between <i>nod</i> gene-harboring bradyrhizobia and <i>nod</i> gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the <i>Bradyrhizobiaceae</i> during ecological adaptation.</p>