Complete genome sequence and phylogenomic analysis of the first N4-like lytic bacteriophage vB_Ppp_A38 (\u03d5A38) infecting Pectobacterium parmentieri

Abstract

Pectobacterium parmentieri (former Pectobacterium wasabiae) is an emerging pectinolytic bacterial pathogen causing losses in potato (Solanum tuberosum L.) worldwide. Until now, there are no effective measures to protect crops from infections caused by P. parmentieri. Likewise, little is known about lytic bacteriophages that can infect and kill P. parmentieri, and that could be used in the (bio)control of this pathogen in agricultural applications. A novel lytic bacteriophage vB_Ppp_A38 (ϕA38), belonging to the order Caudovirales, was isolated and characterised in our previous studies. This report provides information about its complete genome sequence and accompanying phylogenomics. The genome of vB_Ppp_A38 consists of 75,764-bp-length, linear, double-stranded DNA with an average GC content of 48.7% and is predicted to have 97 open reading frames (ORFs), with an average length of 732 nucleotides. The open reading frames were classified into functional groups, including structural units, packing, DNA metabolism, regulation and additional (miscellaneous) functions. Comparative genomic analyses based on the whole-genome sequence indicated that the phage vB_Ppp_A38 is most similar to N4-like viruses of the family Schitoviridae, genus Cbunavirus, sharing more than 90% identity with the phages vB_PatP_CB1, vB_PatP_CB3 and vB_PatP_CB4 infecting P. atrosepticum. The bacteriophage vB_Ppp_A38 is the first Cbunavirus bacteriophage infecting other Pectobacterium spp. hosts than P. atrosepticum. As vB_Ppp_A38 is a lytic virus able to kill plant-pathogenic P. parmentieri, it can be used in the biological control of this pathogen in agricultural applications.