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Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae

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Abstract

Xanthomonas oryzae pv. oryzae (X. oryzae) is a bacterial pathovar of rice diseases all over the world. Owing to emerging antibacterial resistance, phage therapies have gained significant attention to treat various bacterial infections. Nevertheless, comprehensive research is needed for their use as a safe biocontrol agent. In this study, isolation and characterization of a novel phage Xoo-sp15, that infects X. oryzae was ascertained through experimental and bioinformatics analyses to determine its virulent potency and reliability. High throughput sequencing demonstrated that Xoo-sp15 has a dsDNA genome with a total size of 157,091 bp and 39.9% GC content lower than its host (63.6%). Morphological and phylogenetic analyses characterized it as a new member of the Bastille-like group within the family Herelleviridae. In silico analysis revealed that it contains 229 open reading frames and 16 tRNAs. Additionally, this novel phage does not contain any resistant determinants and can infect nine X. oryzae strains. Therefore, Xoo-sp15 has the potential to serve as a novel candidate for phage therapy.

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Acknowledgements

Special thanks to the authors Zhaoxia Dong and Jin Liu for providing help in this study.

Funding

Funding was supported by YFA0903000 (Grant No. YFA0903000).

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Author notes

  1. Amina Nazir, Zhaoxia Dong and Jin Liu have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Sciences, Beijing Institute of Technology, Beijing, China

    Amina Nazir, Rana Adnan Tahir & Hong Qing

  2. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China

    Amina Nazir & Yigang Tong

  3. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, People’s Republic of China

    Zhaoxia Dong, Jin Liu & Donghai Peng

  4. Department of Biosciences, COMSATS University, Sahiwal Campus, Islamabad, Pakistan

    Rana Adnan Tahir

  5. Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constitute College of Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan

    Neelma Ashraf

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  1. Amina Nazir
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Contributions

D.P, H.Q., and Y.T. proposed the idea and designed the experiments. Z.D. and J.L performed the experiments. A.N performed the computational analyses, drafted and wrote the manuscript. R.A.T and N.A critically read, analyzed and revised the manuscript.

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Correspondence to Hong Qing, Donghai Peng or Yigang Tong.

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Supplementary Information

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284_2021_2556_MOESM1_ESM.tif

Supplementary file1 Phage morphology of Xoo-sp15. Phage was negatively stained with 2% phosphotungstic acid (PTA) and examined by transmission electron microscopy (TEM) at an accelerating voltage of 200 kV. The scale bar represents 200 nm. (TIF 9562 kb)

284_2021_2556_MOESM2_ESM.tif

Supplementary file2 Morphology of Xoo-sp15 plaques. Phages were plated in Nutrient Broth agar and overlain with a liquid culture of PXO99A. The plates were incubated at 37 °C. Clear, well-defined Xoo-sp15 plaques were observed and photographed after 36 h. (TIF 1484 kb)

284_2021_2556_MOESM3_ESM.tif

Supplementary file3 Genetic and physical organization of Xoo-sp15 genome. The 229 ORFs of Xoo-sp15 are depicted, and the direction of transcription is indicated by arrows. The G + C content and skew of Xoo-sp15 are also shown. The circle map of the Xoo-sp15 genome was made using CGView (http://wishart.biology.ualberta.ca/cgview/). (TIF 3141 kb)

284_2021_2556_MOESM4_ESM.jpg

Supplementary file4 Comparative genomic analysis of Xoo-sp15 and its homologues. Phages that share over best-hit proteins with Xoo-sp15 were selected and compared using the Easyfig tool. (JPG 3208 kb)

Supplementary file5 (DOCX 81 kb)

Supplementary file6 (DOCX 14 kb)

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Nazir, A., Dong, Z., Liu, J. et al. Isolation, Characterization, and Genome Sequence Analysis of a Novel Lytic Phage, Xoo-sp15 Infecting Xanthomonas oryzae pv. oryzae. Curr Microbiol 78, 3192–3200 (2021). https://doi.org/10.1007/s00284-021-02556-z

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