Archives of Virology

, Volume 163, Issue 7, pp 1977–1980 | Cite as

Genomic characterization and phylogenetic analysis of the novel Pseudomonas phage PPSC2

  • Xiang Wu
  • Yongfeng Wu
  • Ya Tang
  • Bingcheng Gan
Annotated Sequence Record


We isolated a Pseudomonas phage infecting Pseudomonas fluorescens SA1 separated from a soil sample collected in Sichuan Province, China. This phage, which we named PPSC2, has a genome that is composed of a 97,330-bp-long linear double-stranded DNA with 47.51% G+C content and 168 putative protein-coding genes. We identified 20 tRNA genes in the genome of PPSC2, and the tRNA GC content ranged from 44.2% to 58.4%. Phylogenetic and BLASTn analysis revealed that the Pseudomonas phage PPSC2 should be considered a new member of the family Myoviridae.


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

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

Supplementary material

705_2018_3801_MOESM1_ESM.docx (3.1 mb)
Supplementary material 1 (DOCX 3131 kb)
705_2018_3801_MOESM2_ESM.xlsx (23 kb)
Supplementary material 2 (XLSX 23 kb)


  1. 1.
    Euzeby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 47:590–592CrossRefPubMedGoogle Scholar
  2. 2.
    Palleroni NJ (2010) The Pseudomonas story. Environ Microbiol 12:1377–1383CrossRefPubMedGoogle Scholar
  3. 3.
    Thomas JA, Rolando MR, Carroll CA, Shen PS, Belnap DM et al (2008) Characterization of Pseudomonas chlororaphis myovirus 201varphi2-1 via genomic sequencing, mass spectrometry, and electron microscopy. Virology 376:330–338CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Qiao X, Sun Y, Qiao J, Di Sanzo F, Mindich L (2010) Characterization of Phi2954, a newly isolated bacteriophage containing three dsRNA genomic segments. BMC Microbiol 10:55CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Nowicki G, Walkowiak-Nowicka K, Zemleduch-Barylska A, Mleczko A, Frackowiak P et al (2017) Complete genome sequences of two novel autographiviruses infecting a bacterium from the Pseudomonas fluorescens group. Arch Virol 162:2907–2911CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Amgarten D, Martins LF, Lombardi KC, Antunes LP, de Souza APS et al (2017) Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genom 18:346CrossRefGoogle Scholar
  7. 7.
    Adriaenssens EM, Mattheus W, Cornelissen A, Shaburova O, Krylov VN et al (2012) Complete genome sequence of the giant Pseudomonas phage Lu11. J Virol 86:6369–6370CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Uchiyama J, Rashel M, Takemura I, Kato S, Ujihara T et al (2012) Genetic characterization of Pseudomonas aeruginosa bacteriophage KPP10. Arch Virol 157:733–738CrossRefPubMedGoogle Scholar
  9. 9.
    Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE et al (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Loytynoja A (2014) Phylogeny—aware alignment with PRANK. Methods Mol Biol 1079:155–170CrossRefPubMedGoogle Scholar
  15. 15.
    Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256CrossRefPubMedGoogle Scholar
  16. 16.
    Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574CrossRefPubMedGoogle Scholar
  17. 17.
    Fu C, Zhao Q, Li Z, Wang Y, Zhang S et al (2017) Complete genome sequence of Halomonas ventosae virulent halovirus QHHSV-1. Arch Virol 162:3215–3219CrossRefPubMedGoogle Scholar
  18. 18.
    Taylor NM, Prokhorov NS, Guerrero-Ferreira RC, Shneider MM, Browning C et al (2016) Structure of the T4 baseplate and its function in triggering sheath contraction. Nature 533:346–352CrossRefPubMedGoogle Scholar
  19. 19.
    Rao VB, Black LW (2010) Structure and assembly of bacteriophage T4 head. Virol J 7:356CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Black LW, Rao VB (2012) Structure, assembly, and DNA packaging of the bacteriophage T4 head. Adv Virus Res 82:119–153CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Leiman PG, Kanamaru S, Mesyanzhinov VV, Arisaka F, Rossmann MG (2003) Structure and morphogenesis of bacteriophage T4. Cell Mol Life Sci 60:2356–2370CrossRefPubMedGoogle Scholar
  22. 22.
    Abouhmad A, Mamo G, Dishisha T, Amin MA, Hatti-Kaul R (2016) T4 lysozyme fused with cellulose-binding module for antimicrobial cellulosic wound dressing materials. J Appl Microbiol 121:115–125CrossRefPubMedGoogle Scholar
  23. 23.
    Bartell PF, Orr TE, Lam GK (1966) Polysaccharide depolymerase associated with bacteriophage infection. J Bacteriol 92:56–62PubMedPubMedCentralGoogle Scholar
  24. 24.
    Dong TG, Dong S, Catalano C, Moore R, Liang X et al (2015) Generation of reactive oxygen species by lethal attacks from competing microbes. Proc Natl Acad Sci USA 112:2181–2186CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Samaddar S, Grewal RK, Sinha S, Ghosh S, Roy S et al (2015) Dynamics of mycobacteriophage–mycobacterial host interaction: evidence for secondary mechanisms for host lethality. Appl Environ Microbiol 82:124–133CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Hofmann N, Wurm R, Wagner R (2011) The E. coli anti-sigma factor Rsd: studies on the specificity and regulation of its expression. PLoS One 6:e19235CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Borgos SE, Bordel S, Sletta H, Ertesvag H, Jakobsen O et al (2013) Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling. BMC Syst Biol 7:19CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Korolev S (2017) Advances in structural studies of recombination mediator proteins. Biophys Chem 225:27–37CrossRefPubMedGoogle Scholar
  29. 29.
    Bleuit JS, Ma Y, Munro J, Morrical SW (2004) Mutations in a conserved motif inhibit single-stranded DNA binding and recombination mediator activities of bacteriophage T4 UvsY protein. J Biol Chem 279:6077–6086CrossRefPubMedGoogle Scholar
  30. 30.
    Gajewski S, Waddell MB, Vaithiyalingam S, Nourse A, Li Z et al (2016) Structure and mechanism of the phage T4 recombination mediator protein UvsY. Proc Natl Acad Sci USA 113:3275–3280CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Frampton RA, Taylor C, Holguin Moreno AV, Visnovsky SB, Petty NK et al (2014) Identification of bacteriophages for biocontrol of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Appl Environ Microbiol 80:2216–2228CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Rombouts S, Volckaert A, Venneman S, Declercq B, Vandenheuvel D et al (2016) Characterization of novel bacteriophages for biocontrol of bacterial blight in leek caused by Pseudomonas syringae pv. porri. Front Microbiol 7:279CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Xiang Wu
    • 1
    • 3
  • Yongfeng Wu
    • 2
  • Ya Tang
    • 1
  • Bingcheng Gan
    • 3
  1. 1.College of Architecture and EnvironmentSichuan UniversityChengduChina
  2. 2.Sichuan Provincial Transport Department Highway Planning, Survey, Design and Research InstituteChengduChina
  3. 3.Soil and Fertilizer instituteSichuan Academy of Agricultural SciencesChengduChina

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