Comparative Genomics of Bacteriophage of the Genus Seuratvirus.

Pavelas Sazinas,Andrew Millard,Tamsin Redgwell,David J Scanlan,Slawomir Michniewski,Jon Hobman,Aurelija Grigonyte,Branko Rihtman

doi:10.1093/gbe/evx275

Abstract

Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases.

Highlights

Viruses are thought to be the most abundant biological entities on the planet, with an estimated 1031 present in the biosphere (Suttle 2007)
The genomes of the 14 newly isolated bacteriophages were assembled into complete chromosomes that ranged in size from 58.998 kb to 60.165 kb, with a G þ C content that varied from 44.43% to 44.79%
We used the gene encoding a large subunit terminase and DNA polymerase subunit B to determine the phylogeny of these bacteriophages. Both analyses indicated that the isolates from this study are distantly related to bacteriophages of the genus Nonagvirus, but form a monophyletic clade with bacteriophages of the genus Seuratvirus and are part of the Siphoviridae family

Summary

Introduction

Viruses are thought to be the most abundant biological entities on the planet, with an estimated 1031 present in the biosphere (Suttle 2007). The number of genomes of viruses infecting bacteria (bacteriophages) lags well behind those of their hosts (Sepulveda et al 2016; Casey et al 2017; Hatfull 2015). There are currently 400 genomes of bacteriophages within the European Nucleotide Archive (ENA) that infect “Enterobacteria” or Escherichia, compared with the 66,000 Escherichia genomes that are publicly available (https://enterobase.warwick.ac.uk/; last accessed December 28, 2017). The diversity of bacteriophages is exemplified by the number of novel genes found within their genomes with many bacteriophages having little similarity at the genomic level (Pope et al 2015). We isolated and sequenced 14 bacteriophages from a single source of cow slurry gathered from a dairy farm slurry tank in Leicestershire, to expand the diversity and number of bacteriophages that infect Escherichia coli

Methods

Results

Conclusion