Archives of Virology

, Volume 165, Issue 1, pp 215–217 | Cite as

Complete genomic sequence of Pseudomonas lactis bacteriophage HU1 isolated from raw cow’s milk

  • Chikage Tanaka
  • Takahiro Nakayama
  • Takahiro Toba
  • Akiko KashiwagiEmail author
Annotated Sequence Record


The lytic cold-active phage HU1, a member of the family Podoviridae, infects Pseudomonas lactis and was first isolated from raw cow’s milk. In this study, we used deep sequencing to determine and analyze the DNA genome sequence of HU1. We identified a 42,551-base-pair genome comprising double-stranded DNA, with 69 predicted open reading frames and a GC content of 56.4%. A whole-genome comparison did not identify HU1 as a member of any previously reported cluster of Pseudomonas phages. By contrast, HU1 was most similar to AF, which infects P. putida, with nucleotide sequence alignment coverage of 24%. These results suggest that HU1 is a novel Pseudomonas phage.


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

The article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2019_4423_MOESM1_ESM.pdf (132 kb)
Supplementary material 1 (PDF 131 kb)


  1. 1.
    Tanaka C, Yamada K, Takeuchi H, Inokuchi Y, Kashiwagi A, Toba T (2018) A lytic bacteriophage for controlling Pseudomonas lactis in raw cow’s milk. Appl Environ Microbiol 84:e00111–e00118CrossRefGoogle Scholar
  2. 2.
    Zerbino DR (2010) Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 31:11.5.1-11.5.12.Google Scholar
  3. 3.
    Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963CrossRefGoogle Scholar
  4. 4.
    Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679CrossRefGoogle Scholar
  5. 5.
    Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920CrossRefGoogle Scholar
  6. 6.
    Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44(W1):W54–W57CrossRefGoogle Scholar
  7. 7.
    Ha AD, Denver DR (2018) Comparative genomic analysis of 130 bacteriophages infecting bacteria in the genus Pseudomonas. Front Microbiol 9:1456CrossRefGoogle Scholar
  8. 8.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760CrossRefGoogle Scholar
  9. 9.
    Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26CrossRefGoogle Scholar
  10. 10.
    Kiger JA Jr, Sinsheimer RL (1971) DNA of vegetative bacteriophage lambda. VI. Electron microscopic studies of replicating lambda DNA. Proc Natl Acad Sci USA 68:112–115CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
  2. 2.Research Institute of Bio-System InformaticsTohoku Chemical Co., Ltd.MoriokaJapan

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