Complete Genome Sequence of vB_BveP-Goe6, a Virus Infecting Bacillus velezensis FZB42.

The new virus vB_BveP-Goe6 was isolated on the host organism Bacillus velezensis FZB42. The virus morphology indicated its association with the genus Phi29virus The genome of vB_BveP-Goe6 (19,105 bp) comprises a linear chromosome with a GC content of 39.99%. The genome harbors 26 putative protein-coding genes and a noncoding packaging RNA.

GENOME ANNOUNCEMENT

Viruses infecting bacteria are the most abundant biological entities on earth (1) and are ubiquitous in nature (2). Here, the complete genome sequence of the new virus isolate vB_BveP-Goe6 is reported. The naming of the isolate vB_BveP-Goe6 is based on the systematic schema suggested by Kropinski et al. (3). The virus vB_BveP-Goe6 was isolated from the Göttingen municipal sewage plant (Göttingen, Germany, 51°33ʹ15.4ʺN, 9°55ʹ06.4ʺE) via an overlay plaque assay using Bacillus velezensis FZB42 (4, 5) as a host.

Negative-staining transmission electron microscopy of virus particles showed a virion with head tail morphology, typical of the Caudovirales family. The short noncontractive tail revealed that vB_BveP-Goe6 is a member of the Podoviridae family. Virion dimensions of about 50 nm in width and 80 nm in length, together with the specific morphology of its tail, allowed further classification to the Picovirinae subfamily and indicated a relationship to the genus Phi29virus (6).

Viral genomic DNA was prepared with the MasterPure complete DNA and RNA purification kit (Epicentre, Madison, WI, USA). Paired-end Illumina sequencing libraries were generated with the Nextera XT DNA sample preparation kit and were sequenced with a MiSeq instrument and MiSeq reagent kit version 3 (Illumina, San Diego, CA, USA), as recommended by the manufacturer. Trimming and quality filtering of the recovered reads were performed with Trimmomatic version 0.36 (7) and analyzed with FastQC version 0.11.5 (8). The initial assembly was performed with SPAdes version 3.9.0 (9), resulting in a single contig with 1,000-fold coverage. Genome ends were verified via Sanger sequencing (10) and resulted in a final 19,105-bp linear chromosome with a GC content of 39.99%. BLASTn analysis against the nonredundant database of NCBI identified phi29 (GenBank accession no. NC_011048) as the closest relative, with 95% genome sequence identity. Additionally, a significant sequence identity of the vB_BveP-Goe6 genome was also recorded with genomes derived from other members of the Phi29virus genus, such as the viruses PZA (GenBank accession no. M11813), Nf (GenBank accession no. EU622808), B103 (GenBank accession no. NC_004165), and vB_BsuP-Goe1 (GenBank accession no. KU831549) (11). The identified inverted terminal repeats (5ʹ-AAAGTA) of vB_BveP-Goe6 perfectly matched the corresponding ones of other genus members, except virus GA-1 (GenBank accession no. NC_002649). Genome analysis and annotation resulted in the identification of 26 protein-coding genes, of which 18 were with predicted function and 8 were hypothetical proteins. Furthermore, a noncoding RNA could be identified. The annotated genes covered all functions necessary for the replication of a Phi29virus genus member (6). Direct comparison with the genome of phi29 (GenBank accession no. NC_011048) revealed that the genome of vB_BveP-Goe6 is 177 bp smaller. This difference is mainly due to the loss of a hypothetical protein gene located on the left early gene region of vB_BveP-Goe6. The noncoding packaging RNA (pRNA) was identified via a covariance model, which was created with the Infernal 1.1.2 software package (12) using the pRNA genes of virus Nf (GenBank accession no. EU622808) and GA-1 (GenBank accession no. NC_002649) as input sequences. The pRNA is part of the molecular motor, which is responsible for the genome translocation into the prohead.

Accession number(s).

The genome sequence of vB_BveP-Goe6 was deposited in DDBJ/EMBL/GenBank under the accession no. MF407276.