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Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri

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Abstract

Bacteriophage vB_PpaP_PP74 (PP74) is a novel virulent phage that infects members of the species Pectobacterium parmentieri, a newly established species of soft-rot-causing bacteria in the family Pectobacteriaceae, derived from potato-specific Pectobacterium wasabiae. vB_PpaP_PP74 was identified as a member of the family Podoviridae by transmission electron microscopy. The phage has a 39,790-bp dsDNA genome containing 50 open reading frames (ORFs). Because of the absence of genes encoding toxins or lysogeny factors, PP74 may be considered a candidate phage for pathogen biocontrol applications. The genome layout is similar to genomes of T7-like phages within the subfamily Autographivirinae, and therefore, functions can be attributed to most of ORFs. However, the closest nucleotide sequence homologs of phage PP74 are unclassified Escherichia phages. Based on phylogenetic analysis, vB_PpaP_PP74 is a sensu lato T7-like phage, but it forms a distant subgenus group together with homologous enterobacterial phages.

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Nucleotide sequence accession number

The complete genome sequence of phage PP74 have been deposited in the NCBI database under the GenBank accession number KY084243. The draft genome assembly of PB20 strain and related information have been deposited in the NCBI database under the GenBank Accession number PDDJ00000000 (BioProject PRJNA400696).

Funding

This study was supported by Russian Science Foundation Grant #16-16-00073.

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Authors and Affiliations

  1. M.M. Shemyakin-Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia

    Anastasia Kabanova, Mikhail Shneider & Konstantin Miroshnikov

  2. Research Center “PhytoEngineering” Ltd., Rogachevo, Moscow Region, Russia

    Anastasia Kabanova, Eugenia Bugaeva, Vo Thi Ngoc Ha, Alexander Ignatov & Konstantin Miroshnikov

  3. S.N. Winogradsky Institute of Microbiology, Federal Research Center “Fundamental Biotechnology”, Russian Academy of Sciences, Moscow, Russia

    Kirill Miroshnikov & Eugene Kulikov

  4. I. Kant Baltic Federal University, Kaliningrad, Russia

    Aleksei Korzhenkov & Stepan Toschakov

  5. Moscow Institute of Physics and Technology, Moscow, Russia

    Eugene Kulikov & Konstantin Miroshnikov

Authors
  1. Anastasia Kabanova
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  2. Mikhail Shneider
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  3. Eugenia Bugaeva
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  9. Alexander Ignatov
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  10. Konstantin Miroshnikov
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Correspondence to Konstantin Miroshnikov.

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This article does not contain studies with human participants or animals performed by any of the authors.

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Handling Editor: Chan-Shing Lin.

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705_2018_3766_MOESM1_ESM.eps

Supplementary Fig. 1 Phylogenetic analysis of the core genes (RNA polymerase, DNA maturase B, Rz-like lysis protein, and exonuclease) of bacteriophages belonging to the genus T7virus of the subfamily Autographivirinae using the maximum-likelihood method. The phylogenetic reconstruction was made in RAxML ver. 8.2.4 using the LG substitution model and the gamma model of rate heterogeneity. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the nodes (EPS 3862 kb)

Supplementary material 2 (DOCX 31 kb)

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Kabanova, A., Shneider, M., Bugaeva, E. et al. Genomic characteristics of vB_PpaP_PP74, a T7-like Autographivirinae bacteriophage infecting a potato pathogen of the newly proposed species Pectobacterium parmentieri. Arch Virol 163, 1691–1694 (2018). https://doi.org/10.1007/s00705-018-3766-1

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  • DOI: https://doi.org/10.1007/s00705-018-3766-1

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