Complete genome sequences of Gordonia rubripertincta phages OtterstedtS21 and Patos

ABSTRACT We report the genomes of two viruses with siphovirus morphology, OtterstedtS21 and Patos, from Albany, New York, using Gordonia rubripertincta. The genomes of OtterstedtS21 and Patos are ~68 kbp long with 58% GC content. Both phages group with cluster DV based on gene content similarity to phages in the Actinobacteriophage database.

Several members of Gordonia species have been observed to break down hydrocarbons and are thus potential bio-remediators that may be capable of reducing environmental pollution (1).Bacteriophages have also played incredibly important roles in shaping our understanding of microorganisms (2).To further our understanding of the genetic diversity and evolution of Gordonia phages, we report the discovery of two actinobacteriophages, OtterstedtS21 and Patos, which infect G. rubripertincta.
In the fall of 2021, phage OtterstedtS21 was isolated from soil collected from an active construction site near the Albany College of Pharmacy and Health Sciences Campus (42.646943°N, 73.778489°W) and phage Patos from soil collected at Lincoln Park in Albany, New York (42.644879°N, 73.76418°W), using standard procedures (2).In brief, each soil sample was mixed with PYCa (peptone, yeast extract, and calcium) liquid medium, filtered using a 0.22-µm filter, and the filtrate inoculated with G. rubripertincta and incubated with shaking at 30°C.After 2 days, the culture was centrifuged, and the supernatant was screened for phage by plating in PYCa top agar with G. rubripertincta.Both phages were purified through several rounds of plating (2).Transmission electron microscopy revealed both the phages to have siphovirus morphology (Fig. 1; Table 1).
DNA was extracted from OtterstedtS21 and Patos lysates using Wizard DNA Clean-Up Kit (Promega), prepared as sequencing libraries at the University of Pittsburgh Sequenc ing facility using the NEB Ultra-II Library Kit (New England Biolabs), and sequenced using an Illumina MiSeq (v3 reagents) to generate 150 base single-end reads as shown in Table 1.Raw reads were then assembled using Newbler v2.9 and verified for accuracy using Consed v29 (3).Both phages have circularly permuted genomes that share 95.2% nucleotide identity with each other (Table 1).
OtterstedtS21 and Patos are predicted to encode 98 and 102 protein-coding genes, respectively, all on the same strand, with no predicted tRNAs.Both phages share 91% gene content similarity (GCS) and, based on GCS of >35% to phages in the Actino bacteriophage database (phagesDB.org),both phages are grouped into bacteriophage cluster DV (15,16).One half of both genomes encode virus structure and assembly functions, whereas the other half encodes for functions involved in DNA metabolism.Patos encodes for a DNA binding protein (gp64) and an HNH endonuclease (gp83) that are not present in OtterstedtS21.No immunity repressor or integrase functions could be identified in either phage, consistent with other cluster DV phages which suggest that neither phage is likely to establish lysogeny.

TABLE 1
Characteristics of cluster DV siphoviruses OtterstedtS21 and Patos