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Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici strain PRF 81

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Abstract

Rhizobium tropici is representative of the diversity of tropical rhizobia, besides comprising strains very effective in fixing N2 in symbiosis with the common bean (Phaseolus vulgaris L.). The genome of a Brazilian commercial inoculant R. tropici strain (PRF 81, =SEMIA 4088), estimated at 7.85 Mb, was analyzed through a total of 9,026 shotgun reads, assembled in 1,668 phrap contigs, and covering ≈30% of the genome. Annotation identified 2,135 coding DNA sequences (CDS), and only 57.2% have possible functions. The genome comprises a mosaic of genes, with CDS showing the highest similarities with 134 microorganisms, none of which represents more than 19% of the CDS with putative known functions. The high saprophytic capacity of PRF 81 may reside in a variety of genes related to transport, biodegradation of xenobiotics, defense, and secretion proteins, many of which were reported for the first time in the present study. Novelty was also found in nodulation (nodG, a double nodIJ system, nodT, nolF, nolG) and capsular polysaccharide genes, showing stronger similarities with Sinorhizobium (=Ensifer) than with the main symbionts of the common bean—R. etli and R. leguminosarum—suggesting that the original host of R. tropici might be another tropical legume or emphasizing the highly promiscuous nature of this rhizobial species.

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Acknowledgments

Reagents were financed by CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, project # 505499/2004-5). The authors thank Daisy R. Binde and Jesiane S.S. Batista (fellows from CNPq # 505946/2004-1) for the laboratory assistance in the sequencing project, and Dr. Fabio O. Pedrosa and Dr. Emanuel M. Souza for scientific advice. F.G.S. Pinto received a Ph.D. fellow from CNPq. L.M.O. Chueire acknowledges a technology fellowship and A.T.R. Vasconcelos and M. Hungria research fellowships from CNPq. F.G. Barcellos is a pos-doc fellow from CAPES. M. Megías acknowledges MEC for the project # AGL2006-13758-C05-01-AGR.

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Author notes

  1. Fabiana G. S. Pinto

    Present address: Universidade Estadual do Oeste do Paraná, Campus Cascavel, CEP 85819-110, Cascavel, Paraná, Brazil

Authors and Affiliations

  1. Embrapa Soja, Cx. Postal 231, CEP 86001-970, Londrina, Paraná, Brazil

    Fabiana G. S. Pinto, Ligia M. O. Chueire, Pâmela Menna, Fernando G. Barcellos & Mariangela Hungria

  2. Department of Microbiology, Universidade Estadual de Londrina, Londrina, Brazil

    Fabiana G. S. Pinto, Pâmela Menna, Fernando G. Barcellos & Mariangela Hungria

  3. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq-MCT), Brasilia, Brazil

    Fabiana G. S. Pinto, Ligia M. O. Chueire, Ana Tereza R. Vasconcelos, Pâmela Menna & Mariangela Hungria

  4. Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, CEP 25651-071, Petrópolis, Rio de Janeiro, Brazil

    Ana Tereza R. Vasconcelos, Marisa F. Nicolás, Luiz G. P. Almeida & Rangel C. Souza

  5. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasilia, Brazil

    Fernando G. Barcellos

  6. Facultad de Farmacia, Univ. Sevilla, Apdo. Postal 874, 41080, Sevilla, Spain

    Manuel Megías

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  1. Fabiana G. S. Pinto
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  2. Ligia M. O. Chueire
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  3. Ana Tereza R. Vasconcelos
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Correspondence to Mariangela Hungria.

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Pinto, F.G.S., Chueire, L.M.O., Vasconcelos, A.T.R. et al. Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici strain PRF 81. Funct Integr Genomics 9, 263–270 (2009). https://doi.org/10.1007/s10142-009-0109-z

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