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Complete genome sequencing and characterization of single-stranded DNA Vibrio parahaemolyticus phage from inland saline aquaculture environment

A Correction to this article was published on 15 June 2022

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Abstract

Despite their evolutionary, molecular biology and biotechnological significance, relatively fewer numbers of single-stranded DNA (ssDNA) filamentous phages belonging to the family Inoviridae have been discovered and characterized to date. The present study focused on genome sequencing and characterization of an ssDNA Vibrio parahaemolyticus phage V5 previously isolated from an inland saline shrimp culture farm. The complete circular genome of phage V5 consisted of 6658 bp with GC content of 43.7%. During BLASTn analysis, only 36% of phage V5 genome matched with other Vibrio phage genomes in the NCBI database with a sequence identity value of 79%. During the phylogenetic analysis, phage V5 formed a separate branch in the minor clade. These features indicate the novel nature of the phage V5 genome. Among 10 predicted open reading frames (ORFs) in the phage V5 genome, 6 encoded for the proteins of known biological functions, whereas the rest were classified as hypotheticals. Proteins involved in replication and structural assembly were encoded by the phage genome. However, the absence of genes encoding for DNA/RNA polymerases and tRNAs signified that phage V5 is dependent on the host`s molecular machinery for its propagation. As per our knowledge, this is the first study describing the novel genome sequence of an ssDNA V. parahaemolyticus phage from the inland saline environment.

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Fig. 1

accessed from supplementary Table 1

Fig. 2

Data availability

The complete genome sequence and annotation data of V. parahaemolyticus phage V5 is available in the NCBI GenBank database (Accession No. OL512807).

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References

  1. Tyagi A, Saravanan V, Karunasagar I, Karunasagar I (2009) Detection of Vibrio parahaemolyticus in tropical shellfish by SYBR green real-time PCR and evaluation of three enrichment media. Int J Food Microbiol 129:124–130

    CAS  Article  Google Scholar 

  2. Tran L, Nunan L, Redman RM, Mohney LL, Pantoja CR, Fitzsimmons K, Lightner DV (2013) Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp. Dis Aquat Organ 105:45–55

    Article  Google Scholar 

  3. Kumar V, Roy S, Behera BK, Bossier P, Das BK (2021) Acute Hepatopancreatic Necrosis Disease (AHPND): virulence, pathogenesis and mitigation strategies in shrimp aquaculture. Toxins (Basel) 13

  4. Singh B, Tyagi A, Billekallu Thammegowda NK, Ansal MD (2018) Prevalence and antimicrobial resistance of vibrios of human health significance in inland saline aquaculture areas. Aquacult Res 49:2166–2174

    CAS  Article  Google Scholar 

  5. Le Roux F, Wegner KM, Baker-Austin C, Vezzulli L, Osorio CR, Amaro C, Ritchie JM, Defoirdt T, Destoumieux-Garzon D, Blokesch M, Mazel D, Jacq A, Cava F, Gram L, Wendling CC, Strauch E, Kirschner A, Huehn S (2015) The emergence of Vibrio pathogens in Europe: ecology, evolution, and pathogenesis (Paris, 11–12th March 2015). Front Microbiol 6:830

    PubMed  PubMed Central  Google Scholar 

  6. Elmahdi S, DaSilva LV, Parveen S (2016) Antibiotic resistance of Vibrio parahaemolyticus and Vibrio vulnificus in various countries: a review. Food Microbiol 57:128–134

    CAS  Article  Google Scholar 

  7. Brussow H, Hendrix RW (2002) Phage genomics: small is beautiful. Cell 108:13–16

    CAS  Article  Google Scholar 

  8. Haq IU, Chaudhry WN, Akhtar MN, Andleeb S, Qadri I (2012) Bacteriophages and their implications on future biotechnology: a review. Virol J 9:9

    Article  Google Scholar 

  9. Székely AJ, Breitbart M (2016) Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett 363

  10. Dubey S, Singh A, Kumar BTN, Singh NK, Tyagi A (2021) Isolation and characterization of bacteriophages from inland saline aquaculture environments to control Vibrio parahaemolyticus contamination in shrimp. Indian J Microbiol 61:212–217

    CAS  Article  Google Scholar 

  11. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data.

  12. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    CAS  Article  Google Scholar 

  13. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  Article  Google Scholar 

  14. Rai S, Tyagi A, Kumar BTN, Singh NK, Kaur S (2019) Isolation, genomic characterization and stability study of narrow-host range Aeromonas hydrophila lytic bacteriophage. J Exp Zool India 22:1075–1082

    Google Scholar 

  15. Vasimuddin M, Misra S, Li H, Aluru S (2019) Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In: 2019 IEEE international parallel and distributed processing symposium (IPDPS), pp 314–324

  16. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26

    CAS  Article  Google Scholar 

  17. Moraru C, Varsani A, Kropinski AM (2020) VIRIDIC—a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12:1268

    CAS  Article  Google Scholar 

  18. McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R (2018) Phage genome annotation using the RAST pipeline. Methods Mol Biol 1681:231–238

    CAS  Article  Google Scholar 

  19. Contreras-Moreira B, Vinuesa P (2013) GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 79:7696–7701

    CAS  Article  Google Scholar 

  20. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    CAS  Article  Google Scholar 

  21. Horiuchi K (1997) Initiation mechanisms in replication of filamentous phage DNA. Genes Cells 2:425–432

    CAS  Article  Google Scholar 

  22. Stassen AP, Folmer RH, Hilbers CW, Konings RN (1994) Single-stranded DNA binding protein encoded by the filamentous bacteriophage M13: structural and functional characteristics. Mol Biol Rep 20:109–127

    CAS  Article  Google Scholar 

  23. Davis BM, Waldor MK (2000) CTXphi contains a hybrid genome derived from tandemly integrated elements. Proc Natl Acad Sci USA 97:8572–8577

    CAS  Article  Google Scholar 

  24. Mai-Prochnow A, Hui JGK, Kjelleberg S, Rakonjac J, McDougald D, Rice SA (2015) Big things in small packages: the genetics of filamentous phage and effects on fitness of their host. FEMS Microbiol Rev 39:465–487

    Article  Google Scholar 

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Acknowledgements

The authors are grateful to the Dean, College of Fisheries, Guru Angad Dev Veterinary & Animal Sciences University, Ludhiana, India for facilities and support. This work was funded by RKVY Grant “Development of biotechnological intervention strategies to enhance the safety and shelf life of fishery products” (RKVY-11:I3) to Anuj Tyagi, and Indian Council of Agricultural Research (ICAR) Grant under the Niche Area of Excellence on “Antibiotic Resistance: Animal Human Interface” (Edn.10(8)/2016-EP&HS) to A. K. Arora.

Funding

Funding was provided by Indian Council of Agricultural Research (Edn.10(8)/2016-EP&HS) and Rashtriya Krishi Vikas Yojana (RKVY-11:I3).

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Correspondence to Anuj Tyagi.

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The original online version of this article was revised: the figure captions of Figs. 1 and 2 has been corrected.

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Tyagi, A., Dubey, S., Sharma, C. et al. Complete genome sequencing and characterization of single-stranded DNA Vibrio parahaemolyticus phage from inland saline aquaculture environment. Virus Genes (2022). https://doi.org/10.1007/s11262-022-01913-9

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Keywords

  • Shrimp
  • Vibrio parahaemolyticus
  • Phage
  • Inoviridae
  • Genome sequencing