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The complete genomic sequence of the novel myovirus RP13 infecting Ralstonia solanacearum, the causative agent of bacterial wilt

Abstract

A novel lytic bacteriophage, Ralstonia phage RP13, was isolated from tomato fields in Pang Nga, Thailand. Electron microscopic observation showed it to have the features of a myovirus with a novel triangulation number (T = 21, dextro). The RP13 DNA appeared to be heavily modified. By applying RNA sequencing and RNA-sequence-mediated DNA sequencing, the whole genome of RP31 was determined to be 170,942 bp in length with a mean G+C content of 39.2%. A total of 277 ORFs were identified as structural, functional, or hypothetical genes in addition to four tRNA genes. Phylogenetic analysis suggested that RP13 is not closely related to any other known phages. Thus, we concluded that the RP13 is a novel phage infecting R. solanacearum strains and will be a useful biocontrol agent against bacterial wilt disease.

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References

  1. Hayward AC (1991) Biology and epidemiology of bacterial wilt caused by Pseudomonas solanacearum. Annu Rev Phytopathol 29:65–87. https://doi.org/10.1146/annurev.py.29.090191.000433

    CAS  Article  PubMed  Google Scholar 

  2. Hayward AC (2000) Ralstonia solanacearum. In: Lederberg J (ed) Encyclopedia of microbiology, vol 4. Academic Press, San Diego, pp 32–42

    Google Scholar 

  3. Fegan M, Prior P (2005) How complex is the ‘‘Ralstonia solanacearum species complex’’? In: Allen C, Prior P, Hayward AC (eds) Bacterial wilt disease and the Ralstonia solanacearum species complex. APS Press, St. Paul, pp 449–461

    Google Scholar 

  4. Prior P, Ailloud F, Dalsing BL et al (2016) Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species. BMC Genom 17:90

    Article  Google Scholar 

  5. Bhunchoth A, Phironrit N, Leksomboon C et al (2018) Isolation and characterization of bacteriophages that infect Ralstonia solanacearum in Thailand. ISHS Acta Horticulturae 1207. In: V international symposium on tomato diseases: perspectives and future directions in tomato protection, pp 155–162. https://doi.org/10.17660/ActaHortic.2018.1207.20

  6. Neumann E, Kawasaki T, Effantin G et al (2020) 3D structure of three jumbo phage heads. J Gen Virol. https://doi.org/10.1099/jgv.0.001487

    Article  PubMed  Google Scholar 

  7. Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27(19):3911–3920

    CAS  Article  Google Scholar 

  8. Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60

    CAS  Article  Google Scholar 

  9. Wang X, Wei Z, Yang K (2019) Phage combination therapies for bacterial wilt disease in tomato. Nat Biotechnol 37:1513–1529

    CAS  Article  Google Scholar 

  10. Stothard F, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539

    CAS  Article  Google Scholar 

Download references

Acknowledgements

The authors are grateful to D. Yasuda and A. Bhunchoth for host range experiments.

Funding

This study was supported by the Strategic Japanese-Thai Research Cooperative Program (SICP) on Biotechnology (JST/BIOTEC-SICPTH2012) and the Japan Society for the Promotion of Science, KAKENHI (Grant number 15H04477).

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Contributions

TY and TK conceived and designed the research. TK determined the RP13 genomic sequence. HE and HO were responsible for the genomic annotation and phylogenetic analyses. OC did experiments on phage isolation and characterization. TY and TK wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Takashi Yamada.

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Kawasaki, T., Endo, H., Ogata, H. et al. The complete genomic sequence of the novel myovirus RP13 infecting Ralstonia solanacearum, the causative agent of bacterial wilt. Arch Virol 166, 651–654 (2021). https://doi.org/10.1007/s00705-020-04893-z

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  • DOI: https://doi.org/10.1007/s00705-020-04893-z