Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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–e00118
Zerbino DR (2010) Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 31:11.5.1-11.5.12.
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:e112963
Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679
Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920
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–W57
Ha AD, Denver DR (2018) Comparative genomic analysis of 130 bacteriophages infecting bacteria in the genus Pseudomonas. Front Microbiol 9:1456
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26
Kiger JA Jr, Sinsheimer RL (1971) DNA of vegetative bacteriophage lambda. VI. Electron microscopic studies of replicating lambda DNA. Proc Natl Acad Sci USA 68:112–115
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
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.
Additional information
Handling Editor: Johannes Wittmann.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Repository
DNA Data Bank of Japan (DDBJ) accession number AP019415.2.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Tanaka, C., Nakayama, T., Toba, T. et al. Complete genomic sequence of Pseudomonas lactis bacteriophage HU1 isolated from raw cow’s milk. Arch Virol 165, 215–217 (2020). https://doi.org/10.1007/s00705-019-04423-6
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-019-04423-6