Genome sequencing of phages infecting plant associated Enterobacter species

Abstract

Management of plant pathogenic bacteria has been complicated in recent years by a lack of options and chemical resistance in pathogen populations. Viruses that infect bacteria (Bacteriophages) are an emerging target for future biocontrol efforts of plant pathogenic bacteria. The use of bacteriophages in this capacity is still in its infancy, and many challenges exist at each stage of developing a viable biocontrol tool. After isolating phage particles, the next step is identifying and characterising a pure phage lysate. Recent work on bacteriophages of soft rot bacteria resulted in a collection of phage isolates with characterised activity and genome structure. A number of phages are described with complete genomes, generally within the Caudoviricetes. The challenges in effectively sequencing and describing phage genomes require specific strategies to overcome; sufficient phage particle concentration, purity and DNA quality are achieved through large propagations with precipitation and phenol/ chloroform extractions. A workflow using the Oxford Nanopore sequencing platform is presented here as a protocol for identifying and describing bacteriophages that have potential as biocontrol for plant pathogenic bacteria.