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Complete genome analysis of the novel Edwardsiella tarda phage vB_EtaM_ET-ABTNL-9

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Abstract

This work describes the characterization and genome annotation of a new lytic phage, vB_EtaM_ET-ABTNL-9 (referred to as PETp9), isolated from waste water samples collected in Dalian, China, that can kill bacteria of the species Edwardsiella tarda. The genome of phage PETp9 is a circular double-stranded DNA molecule that is 89,762 bp in length with a G+C content of 37.26%, contains 132 ORFs, and encodes one tRNA. Phylogenetic analysis indicated that phage PETp9 should be considered a novel phage.

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References

  1. Austin B, Austin DA (1999) Characteristics of the diseases. In: Austin B, Austin DA (eds) Bacterial fish pathogens: diseases of farmed and wild fish, 3rd edn. Springer-Verlag, Heidelberg, pp 13–15

    Google Scholar 

  2. Evans JJ, Klesius PH, Plumb JA, Shoemaker CA, Han CH (2011) Edwardsiella septicaemias. In: Woo PTK, Bruno DW, Han CH (eds) Fish diseases and disorders: viral, bacterial and fungal infections, volume 3, 2nd edn. CAB International, London, pp 512–569

    Chapter  Google Scholar 

  3. Sakazaki R (2001) Genus XI. Edwarsiella Ewing and McWhorter 1965, 37AL. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, volume 2, 2nd edn. Springer, New York, pp 657–661

    Google Scholar 

  4. Zhang WH, Mi ZQ, Yin XY, Fan H, An XP, Zhang ZY, Chen JK, Tong YG (2013) Characterization of Enterococcus faecalis phage IME-EF1 and its endolysin. Plos One 8:e80435. https://doi.org/10.1371/journal.pone.0080435

    Article  CAS  PubMed Central  Google Scholar 

  5. Sambrook J, Russell DW, Nina I, Kaaren AJ (2001) Chapter 2: Bacteriophage λ and its vectors. In: Sambrook J, Russell DW (eds) Molecular cloning: a laboratory manual, vol 1, 3rd edn. Cold Spring Harbor, New York, pp 2.56

    Google Scholar 

  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  CAS  PubMed Central  Google Scholar 

  7. 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–W689. https://doi.org/10.1093/nar/gki366

    Article  CAS  PubMed Central  Google Scholar 

  8. Zhang XLL, Wang YH, Li SS, An XP, Pei GQ, Huang Y, Fan H, Mi ZQ, Zhang ZY, Wang W, Chen YB, Tong YG (2015) A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini. BMC Genom 16:414. https://doi.org/10.1186/s12864-015-1612-3

    Article  CAS  Google Scholar 

  9. Bebeacua C, Lorenzo Fajardo JC, Blangy S, Spinelli S, Bollmann S, Neve H, Cambillau C, Heller KJ (2013) X-ray structure of a superinfection exclusion lipoprotein from phage TP-J34 and identification of the tape measure protein as its target. Mol Microbiol 89:152–165. https://doi.org/10.1111/mmi.12267

    Article  CAS  Google Scholar 

  10. Dwivedi B, Xue BJ, Lundin D, Edwards RA, Breitbart M (2013) A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol 13:33. https://doi.org/10.1186/1471-2148-13-33

    Article  CAS  PubMed Central  Google Scholar 

  11. 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. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed Central  Google Scholar 

  12. Penadés JR, Chen J, Quiles-Puchalt N, Carpena N, Novick RP (2015) Bacteriophage-mediated spread of bacterial virulence genes. Curr Opin Microbiol 23:171–178. https://doi.org/10.1016/j.mib.2014.11.019

    Article  CAS  Google Scholar 

  13. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. https://doi.org/10.1093/jac/dks261

    Article  CAS  PubMed Central  Google Scholar 

  14. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52:1501–1510. https://doi.org/10.1128/JCM.03617-13

    Article  CAS  PubMed Central  Google Scholar 

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Correspondence to Yongping Xu.

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Cui, H., Zhang, J., Cong, C. et al. Complete genome analysis of the novel Edwardsiella tarda phage vB_EtaM_ET-ABTNL-9. Arch Virol 165, 1241–1244 (2020). https://doi.org/10.1007/s00705-020-04600-y

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  • DOI: https://doi.org/10.1007/s00705-020-04600-y

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