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YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing

1
Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 UH Helsinki, Finland
2
Applied Sciences, University of Northumbria, Newcastle upon Tyne NE1 8ST, UK
3
Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(6), 620; https://doi.org/10.3390/v12060620
Received: 17 January 2020 / Revised: 25 May 2020 / Accepted: 4 June 2020 / Published: 5 June 2020
(This article belongs to the Section Bacterial Viruses)
YerA41 is a Myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified in such a way that it is an unsuitable template for PCR amplification and for conventional sequencing. To determine the YerA41 genome sequence, we performed RNA-sequencing from phage-infected Y. ruckeri cells at different time points post-infection. The host-genome specific reads were subtracted and de novo assembly was performed on the remaining unaligned reads. This resulted in nine phage-specific scaffolds with a total length of 143 kb that shared only low level and scattered identity to known sequences deposited in DNA databases. Annotation of the sequences revealed 201 predicted genes, most of which found no homologs in the databases. Proteome studies identified altogether 63 phage particle-associated proteins. The RNA-sequencing data were used to characterize the transcriptional control of YerA41 and to investigate its impact on the bacterial gene expression. Overall, our results indicate that RNA-sequencing can be successfully used to obtain the genomic sequence of non-sequencable phages, providing simultaneous information about the phage–host interactions during the process of infection. View Full-Text
Keywords: YerA41; bacteriophage; RNA-sequencing; nucleotide modification; genome assembly; transcriptome; Yersinia ruckeri YerA41; bacteriophage; RNA-sequencing; nucleotide modification; genome assembly; transcriptome; Yersinia ruckeri
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MDPI and ACS Style

Leskinen, K.; Pajunen, M.I.; Vilanova, M.V.G.-R.; Kiljunen, S.; Nelson, A.; Smith, D.; Skurnik, M. YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing. Viruses 2020, 12, 620. https://doi.org/10.3390/v12060620

AMA Style

Leskinen K, Pajunen MI, Vilanova MVG-R, Kiljunen S, Nelson A, Smith D, Skurnik M. YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing. Viruses. 2020; 12(6):620. https://doi.org/10.3390/v12060620

Chicago/Turabian Style

Leskinen, Katarzyna, Maria I. Pajunen, Miguel V.G.-R. Vilanova, Saija Kiljunen, Andrew Nelson, Darren Smith, and Mikael Skurnik. 2020. "YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing" Viruses 12, no. 6: 620. https://doi.org/10.3390/v12060620

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