Genomic hypervariability of phage Andromeda is unique among known dsDNA viruses

Abstract

A new lytic bacteriophage Andromeda, specific to the economically important plant pathogen Pseudomonas syringae, was isolated and characterised. It belongs to the Podoviridae family, Autographivirinae subfamily and possesses a linear dsDNA genome of 40,008 bp with four localised nicks. Crucially, Andromeda's genome has no less than 80 hypervariable sites (SNPs), which show genome wide distribution resulting in heterogenous populations of this phage reminiscent of those of RNA virus quasispecies.Andromeda has no nucleotide sequence homology to phage phiNFS, a member of phiKMVviruses, in which a similar phenomenon was discovered. We show that Andromeda and Andromeda-related phages form a group within the Autographivirinae, designated here as the "ExophiKMVviruses". The "ExophiKMVviruses" were revealed to share conservation of gene order with core phiKMVviruses despite their sequence-based relationship to SP6-related phages. Our findings suggest that genomic hypervariability might be a feature that occurs among various Autographivirinae groups.

The Bacteriophage Pf-10—A Component of the Biopesticide “Multiphage” Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae

“…The adsorption constant of phage Pf-10 calculated using the equation described by Kropinski [45] is (3.59 ± 1.42) × 10 −9 mL/min. The adsorption rate of phage Pf-10 was similar to that of other reported Pseudomonas-infecting phages of the Autographiviridae family, namely: Pseudomonas phage Andromeda (1.48 × 10 −9 mL/min) [63] and Pseudomonas phage PAXYB1 (3.70 × 10 −9 mL/min) [64].…”

“…The latency period of the Pf-10 phage was nearly similar to Pseudomonas phage gh-1 (21 min) [65], and shorter than that of most Pseudomonas phages of the Autographiviridae family, namely Pseudomonas phage Andromeda (25-30 min) [63], Pseudomonas phage PAXYB1 (30 min) [64] and Pseudomonas phage RLP (25 min) [66], and especially of Pseudomonas phage BF7, which shows an extremely long latent period (140 min) [67]. Interestingly, the burst size of Pf-10 was smaller than that of other reported Pseudomonas phages of the Autographiviridae family such as Pseudomonas phage gh-1 (103 PFU) [65], Pseudomonas phage Andromeda (70 PFU) [63], Pseudomonas phage PAXYB1 (141 PFU) [64], Pseudomonas phage RLP (154 PFU) [66] and Pseudomonas phage BF7 (237 PFU) [67]. However, it should also be noted that all time and kinetic parameters of phage adsorption and one-step growth curve may differ depending on the bacterial host.…”

Biological and Molecular Characterization of the Lytic Bacteriophage SoKa against Pseudomonas syringae pv. syringae, Causal Agent of Citrus Blast and Black Pit in Tunisia

“…The SoKa genome was determined using whole genome sequencing. This revealed a dsDNA genome of 40,360 bp, with BLASTn similarity to Pseudomonas phages BIM BV-45 (MT094430; 96% coverage; 94.67% identity), Andromeda [41] (KX458241; 97% coverage; 96.76% identity), and Bf7 [42] (JN991020; 86% coverage; 83.22% identity). To classify SoKa, the intergenomic distance to related bacteriophages (identified with a Viptree proteome analysis) was calculated and plotted (Figure 3).…”