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Complete genome sequence of a novel lytic bacteriophage, PLG-II, specific for Lactococcus garvieae serotype II strains that are pathogenic to fish

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Abstract

A novel lytic siphophage, PLG-II, which is specific for Lactococcus garvieae serotype II strains that are pathogenic to fish, was isolated from seawater samples collected from Miyazaki Prefecture, Japan. Whole-genome sequencing showed that the PLG-II genome is a 32,271-bp double-stranded DNA molecule, with an average GC content of 37.74%. It contains 69 open reading frames (ORFs), 43 of which currently have no reliable functional annotation for their product, as well as a single tRNA. Comparative genomics analysis suggests that phage PLG-II might represent a novel species in the genus Uwajimavirus.

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References

  1. Ohbayashi K, Oinaka D, Hoai TD et al (2017) PCR-mediated identification of the newly emerging pathogen Lactococcus garvieae serotype II from Seriola quinqueradiata and S. dumerili. Fish Pathol 52:46–49. https://doi.org/10.3147/jsfp.52.46

    Article  Google Scholar 

  2. Nishiki I, Furukawa M, Matui S et al (2011) Epidemiological study on Lactococcus garvieae isolates from fish in Japan. Fish Sci 77:367–373. https://doi.org/10.1007/s12562-011-0332-0

    Article  CAS  Google Scholar 

  3. Oinaka D, Yoshimura N, Fukuda Y et al (2015) Isolation of Lactococcus garvieae showing no agglutination with anti-KG-phenotype rabbit serum. Fish Pathol 50:37–43. https://doi.org/10.3147/jsfp.50.37

    Article  Google Scholar 

  4. Fukuda Y, Tue Y, Oinaka D et al (2015) Pathogenicity and immunogenicity of non-agglutinating Lactococcus garvieae with anti-KG-phenotype rabbit serum in Seriola spp. Fish Pathol 50:200–206. https://doi.org/10.3147/jsfp.50.200

    Article  Google Scholar 

  5. Shi YZ, Nishiki I, Yanagi S, Yoshida T (2019) Epidemiological study on newly emerging lactococcus garvieae serotype ii isolated from marine fish species in japan. Fish Pathol 54:51–57. https://doi.org/10.3147/jsfp.54.51

    Article  Google Scholar 

  6. Mirzaei MK, Nilsson AS (2015) Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS ONE 10:e0118557. https://doi.org/10.1371/JOURNAL.PONE.0118557

    Article  Google Scholar 

  7. Park KH, Matsuoka S, Nakai T, Muroga K (1997) A virulent bacteriophage of Lactococcus garvieae (formerly Enterococcus seriolicida) isolated from yellowtail Seriola quinqueradiata. Dis Aquat Org 29:145–149. https://doi.org/10.3354/dao029145

    Article  Google Scholar 

  8. Park KH, Kato H, Nakai T, Muroga K (1998) Phage typing of lactococcus garvieae (formerly enterococcus seriolicida) a pathogen of cultured yellowtail. Fish Sci 64:62–64. https://doi.org/10.2331/fishsci.64.62

    Article  CAS  Google Scholar 

  9. Nakai T, Sugimoto R, Park KH et al (1999) Protective effects of bacteriophage on experimental Lactococcus garvieae infection in yellowtail. Dis Aquat Organ 37:33–41. https://doi.org/10.3354/dao037033

    Article  CAS  PubMed  Google Scholar 

  10. Gencay YE, Birk T, Sørensen MCH, Brøndsted L (2017) Methods for isolation, purification, and propagation of bacteriophages of Campylobacter jejuni. Methods Mol Biol 1512:19–28. https://doi.org/10.1007/978-1-4939-6536-6_3

    Article  PubMed  Google Scholar 

  11. Hoai T, Nishiki I, Yoshida T, Nakai T (2018) Host range and influence of a cell capsule on the phage efficacy of three Lactococcus garvieae lytic phages. Dis Aquat Org 128:81–86

    Article  CAS  Google Scholar 

  12. Andrews S (2010) FastQC—A quality control tool for high throughput sequence data. accessed on 20th March 2021  http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 

  13. Bushnell B (2014) BBMap: a fast, accurate, splice-aware aligner. In: Conference 9th annual genomics of energy & environment meeting, Walnut Creek, CA, March 17–20, 2014

  14. Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:1–22. https://doi.org/10.1371/journal.pcbi.1005595

    Article  CAS  Google Scholar 

  15. Altschup SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  Google Scholar 

  16. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm009

    Article  PubMed  PubMed Central  Google Scholar 

  17. Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:451–454. https://doi.org/10.1093/nar/gki487

    Article  CAS  Google Scholar 

  18. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16. https://doi.org/10.1093/nar/gkh152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/NAR/25.5.955

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Pope WH, Jacobs-Sera D (2018) Annotation of bacteriophage genome sequences using DNA master: an overview. In: Methods in molecular biology. Humana Press Inc., pp 217–229

  21. Zrelovs N, Dislers A, Kazaks A (2021) Genome characterization of nocturne116, novel lactococcus lactis-infecting phage isolated from moth. Microorg. 9:1540. https://doi.org/10.3390/MICROORGANISMS9071540

    Article  CAS  Google Scholar 

  22. Moraru C, Varsani A, Viruses AK-2020 U (2020) VIRIDIC—a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. mdpi.com 12

  23. Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. https://doi.org/10.1038/MSB.2011.75

    Article  PubMed  PubMed Central  Google Scholar 

  24. Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/MOLBEV/MSU300

    Article  CAS  PubMed  Google Scholar 

  25. Kalyaanamoorthy S, Minh BQ, Wong TKF et al (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 146(14):587–589. https://doi.org/10.1038/nmeth.4285

    Article  CAS  Google Scholar 

  26. Minh BQ, Nguyen MAT, Von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195. https://doi.org/10.1093/MOLBEV/MST024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010. https://doi.org/10.1093/BIOINFORMATICS/BTR039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Turner D, Kropinski AM, Adriaenssens EM (2021) A roadmap for genome-based phage taxonomy. Viruses 13:506. https://doi.org/10.3390/V13030506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors are grateful to the Government of Japan for awarding the MEXT scholarship to Muhammad Akmal for his research.

Funding

This study was funded by JSPS KAKENHI Grant Number 21H02287 and 22K19214.

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Authors and Affiliations

  1. Faculty of Agriculture, University of Miyazaki, Gauken Kibanadai Nishi 1-1, Miyazaki, 889-2192, Japan

    Muhammad Akmal, Issei Nishiki & Terutoyo Yoshida

  2. Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan

    Muhammad Akmal

  3. Latvian Biomedical Research and Study Centre, Ratsupites 1 k1, Riga, 1067, Latvia

    Nikita Zrelovs

Authors
  1. Muhammad Akmal
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  2. Issei Nishiki
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  4. Terutoyo Yoshida
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Correspondence to Muhammad Akmal.

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Akmal, M., Nishiki, I., Zrelovs, N. et al. Complete genome sequence of a novel lytic bacteriophage, PLG-II, specific for Lactococcus garvieae serotype II strains that are pathogenic to fish. Arch Virol 167, 2331–2335 (2022). https://doi.org/10.1007/s00705-022-05568-7

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  • DOI: https://doi.org/10.1007/s00705-022-05568-7

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