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

Virus Genes (2022)Cite this article

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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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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Authors and Affiliations

  1. College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India

    Anuj Tyagi, Shiwam Dubey, Chetna Sharma, Prapti Sudan, Sumeet Rai & B. T. Naveen Kumar

  2. College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India

    Mudit Chandra & A. K. Arora

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  1. Anuj Tyagi
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  2. Shiwam Dubey
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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