Skip to main content
SpringerLink
Log in

Genome sequence analysis of Vibrio parahaemolyticus lytic phage Vp_R1 with a C3 morphotype

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Phage Vp_R1 belongs to the family Podoviridae and has a C3 morphotype, with an elongated head with a diameter of 190 ± 1.1 nm and an ultrashort tail with a length of 9 ± 1.2 nm. The double-stranded DNA genome is 112.1 kb long, has a mol% G + C content of 40.3, contains 129 ORFs, and encodes four tRNAs. Phylogenetic analysis suggests that phage Vp_R1 is a novel member of the genus Kuravirus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Ackermann HW (2001) Frequency of morphological phage descriptions in the year 2000. Brief review. Arch Virol 146:843–857

    Article  CAS  Google Scholar 

  2. Ackermann HW (2007) 5500 Phages examined in the electron microscope. Arch Virol 152:227–243

    Article  CAS  Google Scholar 

  3. Ceccarelli D, Hasan NA, Huq A, Colwell RR (2013) Distribution and dynamics of epidemic and pandemic Vibrio parahaemolyticus virulence factors. Front Cell Infect Mi 3:97

    Google Scholar 

  4. Chen D, Texada DE (2006) Low-usage codons and rare codons of Escherichia coli mini review. Gene Ther Mol Biol 10:1–12

    Google Scholar 

  5. Chen Y, Liu XM, Yan JW, Li XG, Mei LL, Mao QF, Ma Y (2010) Foodborne pathogens in retail oysters in south China. Biomed Environ Sci 23:32–36

    Article  CAS  Google Scholar 

  6. Chopin A, Deveau H, Ehrlich SD, Moineau S, Chopin M (2007) KSY1, a lactococcal phage with a T7-like transcription. Virology 365:1–9

    Article  CAS  Google Scholar 

  7. Doss J, Culbertson K, Hahn D, Camacho J, Barekzi N (2017) A review of phage therapy against bacterial pathogens of aquatic and terrestrial organisms. Viruses 9:50

    Article  Google Scholar 

  8. Dwivedi B, Xue B, Lundin D, Edwards RA, Breitbart M (2013) A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol 13:33

    Article  CAS  Google Scholar 

  9. Goldsmith DB, Crosti G, Dwivedi B, McDaniel LD, Varsani A, Suttle CA, Weinbauer MG, Sandaa R, Breitbart M (2011) Development of phoH as a novel signature gene for assessing marine phage diversity. Appl Environ Microb 77:7730–7739

    Article  CAS  Google Scholar 

  10. Goodridge L, Gallaccio A, Griffiths MW (2003) Morphological, host range, and genetic characterization of two coliphages. Appl Environ Microb 69:5364–5371

    Article  CAS  Google Scholar 

  11. Harakudo Y, Saito S, Ohtsuka K, Yamasaki S, Yahiro S, Nishio T, Iwade Y, Otomo Y, Konuma H, Tanaka H (2012) Characteristics of a sharp decrease in vibrio parahaemolyticus infections and seafood contamination in Japan. Int J Food Microbiol 157:95–101

    Article  Google Scholar 

  12. Kenshi M, Jumpei U, Shin-Ichiro K, Takako U, Hiroshi H, Shigeyoshi S, Asako M, Hiroshi W, Shigenobu M (2010) Morphological and genetic analysis of three bacteriophages of Serratia marcescens isolated from environmental water. FEMS Microbiol Lett 291:201–208

    Google Scholar 

  13. Kropinski AM, Lingohr EJ, Ackermann H (2011) The genome sequence of enterobacterial phage 7–11, which possesses an unusually elongated head. Arch Virol 156:149–151

    Article  CAS  Google Scholar 

  14. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  15. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  Google Scholar 

  16. Lee JK, Jung DW, Eom SY, Oh SW, Kim Y, Kwak HS, Kim YH (2008) Occurrence of Vibrio parahaemolyticus in oysters from Korean retail outlets. Food Control 19:990–994

    Article  Google Scholar 

  17. Lenneman B, Rothman-Denes L (2015) Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases. Biomolecules 5:647–667

    Article  CAS  Google Scholar 

  18. Li Y, Chen M, Tang F, Yao H, Lu C, Zhang W (2012) Complete genome sequence of the novel lytic avian pathogenic coliphage NJ01. J Virol 86:13874–13875

    Article  CAS  Google Scholar 

  19. Mirzaei MK, Eriksson H, Kasuga K, Haggård-Ljungquist E, Nilsson AS (2014) Genomic, proteomic, morphological, and phylogenetic analyses of vB_EcoP_SU10, a podoviridae phage with C3 morphology. PloS One 9:e116294

    Article  Google Scholar 

  20. Nakai T, Park SC (2002) Bacteriophage therapy of infectious diseases in aquaculture. Res Microbiol 153:13–18

    Article  Google Scholar 

  21. Ren H, Li Z, Xu Y, Wang L, Li X (2019) Protective effectiveness of feeding phage cocktails in controlling Vibrio parahaemolyticus infection of sea cucumber Apostichopus japonicus. Aquaculture 503:322–329

    Article  CAS  Google Scholar 

  22. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, volume 2. Anal Biochem 186:182–183

    Google Scholar 

  23. Savalia D, Westblade LF, Goel M, Florens L, Kemp P, Akulenko N, Pavlova O, Padovan JC, Chait BT, Washburn MP, Ackermann H, Mushegian A, Gabisonia T, Molineux I, Severinov K (2008) Genomic and proteomic analysis of phiEco32, a novel Escherichia coli bacteriophage. J Mol Biol 377:774–789

    Article  CAS  Google Scholar 

  24. Saxelin M, Nurmiaho E, Korhola MP, Sundman V (1979) Partial characterization of a new C3-type capsule-dissolving phage ofStreptococcus cremoris. Can J Microbiol 25:1182–1187

    Article  CAS  Google Scholar 

  25. Zhang L, Orth K (2013) Virulence determinants for Vibrio parahaemolyticus infection. Curr Opin Microbiol 16:70–77

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank the members of the group of Professor Yigang Tong, Beijing Institute of Microbiology and Epidemiology, for help with sequence analysis.

Funding

This work was financially supported by the National Public Science and Technology Research Funds Projects of Ocean (Grant No. 201405003).

Author information

Authors and Affiliations

  1. School of Bioengineering, Dalian University of Technology, Dalian, 116024, People’s Republic of China

    Hongyu Ren, Le Xu, Xiaoyu Li, Lili Wang & Yongping Xu

  2. School of Ocean and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, People’s Republic of China

    Zhen Li

  3. Postdoctoral Work Center in Dalian SEM Biological Engineering Co. Ltd, Dalian, 116620, People’s Republic of China

    Zhen Li & Yongping Xu

Authors
  1. Hongyu Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhen Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Le Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaoyu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lili Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yongping Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yongping Xu.

Ethics declarations

Conflict of interest

There are no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants or animals by any author.

Additional information

Handling Editor: T. K. Frey.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Fig. S1 Secondary structure visualization of tRNAs of Vp_R1. A. tRNA-Met (CAT). B. tRNA–Ile (GAT). C. tRNA- Arg (CCT). D. tRNA-Arg (TCT).

Below is the link to the electronic supplementary material.

Supplementary material 1 (TIFF 1277 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ren, H., Li, Z., Xu, L. et al. Genome sequence analysis of Vibrio parahaemolyticus lytic phage Vp_R1 with a C3 morphotype. Arch Virol 164, 2865–2871 (2019). https://doi.org/10.1007/s00705-019-04364-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-019-04364-0

Search

Navigation