Genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid

Shin Okazaki, Rujirek Noisangiam, Takashi Okubo, Takakazu Kaneko, Kenshiro Oshima, Masahira Hattori, Kamonluck Teamtisong, Pongpan Songwattana, Panlada Tittabutr, Nantakorn Boonkerd, Kazuhiko Saeki, Shusei Sato, Toshiki Uchiumi, Kiwamu Minamisawa, Neung Teaumroong

Research output: Contribution to journalArticle

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Abstract

Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation. Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation.

Original languageEnglish
Article numbere0117392
JournalPLoS One
Volume10
Issue number2
DOIs
Publication statusPublished - 2015 Feb 24
Externally publishedYes

Fingerprint

Bradyrhizobium
nodulation
Bradyrhizobiaceae
plasmids
Plasmids
Genes
Genome
genome
Photorhizobium
genes
protein secretion
Chromosomes
chromosomes
Aeschynomene americana
Aeschynomene
genomic islands
Genomic Islands
Nitrogen Fixation
Host Specificity
Base Composition

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Okazaki, S., Noisangiam, R., Okubo, T., Kaneko, T., Oshima, K., Hattori, M., ... Teaumroong, N. (2015). Genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid. PLoS One, 10(2), [e0117392]. https://doi.org/10.1371/journal.pone.0117392

Genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid. / Okazaki, Shin; Noisangiam, Rujirek; Okubo, Takashi; Kaneko, Takakazu; Oshima, Kenshiro; Hattori, Masahira; Teamtisong, Kamonluck; Songwattana, Pongpan; Tittabutr, Panlada; Boonkerd, Nantakorn; Saeki, Kazuhiko; Sato, Shusei; Uchiumi, Toshiki; Minamisawa, Kiwamu; Teaumroong, Neung.

In: PLoS One, Vol. 10, No. 2, e0117392, 24.02.2015.

Research output: Contribution to journalArticle

Okazaki, S, Noisangiam, R, Okubo, T, Kaneko, T, Oshima, K, Hattori, M, Teamtisong, K, Songwattana, P, Tittabutr, P, Boonkerd, N, Saeki, K, Sato, S, Uchiumi, T, Minamisawa, K & Teaumroong, N 2015, 'Genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid', PLoS One, vol. 10, no. 2, e0117392. https://doi.org/10.1371/journal.pone.0117392
Okazaki, Shin ; Noisangiam, Rujirek ; Okubo, Takashi ; Kaneko, Takakazu ; Oshima, Kenshiro ; Hattori, Masahira ; Teamtisong, Kamonluck ; Songwattana, Pongpan ; Tittabutr, Panlada ; Boonkerd, Nantakorn ; Saeki, Kazuhiko ; Sato, Shusei ; Uchiumi, Toshiki ; Minamisawa, Kiwamu ; Teaumroong, Neung. / Genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid. In: PLoS One. 2015 ; Vol. 10, No. 2.
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abstract = "Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation. Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation.",
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AU - Okazaki, Shin

AU - Noisangiam, Rujirek

AU - Okubo, Takashi

AU - Kaneko, Takakazu

AU - Oshima, Kenshiro

AU - Hattori, Masahira

AU - Teamtisong, Kamonluck

AU - Songwattana, Pongpan

AU - Tittabutr, Panlada

AU - Boonkerd, Nantakorn

AU - Saeki, Kazuhiko

AU - Sato, Shusei

AU - Uchiumi, Toshiki

AU - Minamisawa, Kiwamu

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AB - Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation. Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. 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 nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene 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 nod genes of DOA9 exhibited low similarity with those of other strains. The nif 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 nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation.

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