Abstract
The genomic characterization of phages with biocontrol potential against food-related bacteria is essential to future commercial applications. Here, we report the genome sequence of P. fluorescens phage UFJF_PfSW6 and a taxonomy proposal framing it as a novel phage species with great potential for biocontrol in the dairy industry. It showed a short linear double-stranded DNA genome (~ 39 kb) with a GC content of 21.2% and short DTR sequences of 215 bp. The genome of the UFJF_PfSW6 phage contains 48 genes with a unidirectional organization into three functional modules: DNA replication and metabolism, structural proteins, and DNA packing and host lysis. Thirteen promoters from phage and nine from host regulate these genes, and six Rho-independent terminators control their transcription. Twenty-seven genes of the UFJF_PfSW6 encode proteins with predicted functions. Comparative genome analysis revealed that the UFJF_PfSW6 genome shares 84% of genomic similarity with the genome sequence of the Pijolavirus PspYZU08, the only representative of the genus recognized so far. Therefore, our findings indicate that both phages are of the same genus, but UFJF_PfSW6 a is a novel Pijolavirus specie belonging to the Studiervirinae subfamily.
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Data availability
All data analyzed in this study are available in this published article and its supplementary information files. The complete genome sequence of the P. fluorescens phage UFJF_PfSW6 is publicly available on DDBJ/EMBL/GenBank under accession number OP924544: https://www.ncbi.nlm.nih.gov/nuccore/OP924544.
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Acknowledgements
We thank the Núcleo de Análise de Biomoléculas (NuBioMol) of the Universidade Federal de Viçosa (UFV) for providing the facilities for data analysis. NuBioMol is financially supported by the following Brazilian agencies: Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Financiadora de Estudos e Projetos (Finep) and Sistema Nacional de Laboratórios em Nanotecnologias (SisNANO)/Ministério da Ciência, Tecnologia e Informação (MCTI). We also thank Professor Cristina Dantas Vanetti of the Universidade Federal de Viçosa (UFV) for providing the host bacterial strain (P. fluorescens UFV 041) used in this work.
Funding
This research was funded by Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG), grants numbers CAG00390-15 and APQ00146-22, and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), grant number 427667/2016-0.
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Both authors contributed to this work, wrote, reviewed, and approved the manuscript. The first author executed the genome assembly and analyzed the data. The second author performed the experiments and coordinated the research.
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This article does not contain any studies with human participants or animals performed by any of the authors.
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13205_2023_3485_MOESM1_ESM.pdf
Supplementary file1 (PDF 91 kb): Figure S1. Viral proteomic tree of reference genomes for Studiervirinae subfamily. The proteomic tree includes the genomes of Pseudomonas phage UFJF_fSW6 and 144 species of the Studiervirinae subfamily (taxonomy ID 2731653) available in the NCBI Reference Sequence (RefSeq) database (https://www.ncbi.nlm.nih.gov/refseq). The genomes were aligned all-against-all using ViPTree (https://www.genome.jp/viptree/) to compute the genomic similarity scores (SG) (Table S4). The cluster highlighted in yellow represents the Pijolavirus genus and includes the phage UFJF_fSW6.
13205_2023_3485_MOESM2_ESM.xlsx
Supplementary file2 (XLSX 37 kb): Table S1Annotation of the Pijolavirus ufjfpfsw6 genome.Table S2. Promoters predicted in the Pijolavirus ufjfpfsw6 genome. Table S3. Rho-independent terminators predicted in the Pijolavirus ufjfpfsw6 genome.Table S4. Intergenomic similarities between Pijolavirus ufjfpfsw6 genome and reference genomes for Studiervirinae subfamily (taxonomy ID 2731653) available in the NCBI Reference Sequence (RefSeq) database (https://www.ncbi.nlm.nih.gov/refseq). The genomes were aligned all-against-all using ViPTree (https://www.genome.jp/viptree/) and VIRIDIC (http://rhea.icbm.uni-oldenburg.de/VIRIDIC).Table S5. Similarities calculated by Clincker.
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Vidigal, P.M.P., Hungaro, H.M. Genome sequencing of Pseudomonas fluorescens phage UFJF_PfSW6: a novel lytic Pijolavirus specie with potential for biocontrol in the dairy industry. 3 Biotech 13, 67 (2023). https://doi.org/10.1007/s13205-023-03485-3
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DOI: https://doi.org/10.1007/s13205-023-03485-3