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

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          ABSTRACT

          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.

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          Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp plantarum and 'Bacillus oryzicola' are later heterotypic synonyms of Bacillus velezensis based on phylogenomics

          Christopher A Dunlap, Soo-Jin Kim, Soon-Wo Kwon … (2016)
          Bacillus velezensis was previously reported to be a later heterotypic synonym of Bacillus amyloliquefaciens, based primarily on DNA-DNA relatedness values. We have sequenced a draft genome of B. velezensis NRRL B-41580T. Comparative genomics and DNA-DNA relatedness calculations show that it is not a synonym of B. amyloliquefaciens. It was instead synonymous with Bacillus methylotrophicus. 'Bacillus oryzicola' is a recently described species that was isolated as an endophyte of rice (Oryza sativa). The strain was demonstrated to have plant-pathogen antagonist activity in greenhouse assays, and the 16S rRNA gene was reported to have 99.7 % sequence similarity with Bacillus siamensis and B. methylotrophicus, which are both known for their plant pathogen antagonism. To better understand the phylogenetics of these closely related strains, we sequenced the genome of 'B. oryzicola' KACC 18228. Comparative genomic analysis showed only minor differences between this strain and the genomes of B. velezensis NRRL B-41580T, B. methylotrophicus KACC 13015T and Bacillus amyloliquefaciens subsp. plantarum FZB42T. The pairwise in silico DNA-DNA hybridization values calculated in comparisons between the strains were all greater than 84 %, which is well above the standard species threshold of 70 %. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the strains share phenotype and genotype coherence. Therefore, we propose that B. methylotrophicus KACC 13015T, B. amyloliquefaciens subsp. plantarum FZB42T, and 'B. oryzicola' KACC 18228 should be reclassified as later heterotypic synonyms of B. velezensis NRRL B-41580T, since the valid publication date of B. velezensis precedes the other three strains.
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            Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea.

            Andrew M Kropinski, Rob Lavigne, David Prangishvili (2009)
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              Phi29 family of phages.

              G W Meijer, J Horcajadas, Scarlet M Salas (2001)
              Continuous research spanning more than three decades has made the Bacillus bacteriophage phi29 a paradigm for several molecular mechanisms of general biological processes, such as DNA replication, regulation of transcription, phage morphogenesis, and phage DNA packaging. The genome of bacteriophage phi29 consists of a linear double-stranded DNA (dsDNA), which has a terminal protein (TP) covalently linked to its 5' ends. Initiation of DNA replication, carried out by a protein-primed mechanism, has been studied in detail and is considered to be a model system for the protein-primed DNA replication that is also used by most other linear genomes with a TP linked to their DNA ends, such as other phages, linear plasmids, and adenoviruses. In addition to a continuing progress in unraveling the initiation of DNA replication mechanism and the role of various proteins involved in this process, major advances have been made during the last few years, especially in our understanding of transcription regulation, the head-tail connector protein, and DNA packaging. Recent progress in all these topics is reviewed. In addition to phi29, the genomes of several other Bacillus phages consist of a linear dsDNA with a TP molecule attached to their 5' ends. These phi29-like phages can be divided into three groups. The first group includes, in addition to phi29, phages PZA, phi15, and BS32. The second group comprises B103, Nf, and M2Y, and the third group contains GA-1 as its sole member. Whereas the DNA sequences of the complete genomes of phi29 (group I) and B103 (group II) are known, only parts of the genome of GA-1 (group III) were sequenced. We have determined the complete DNA sequence of the GA-1 genome, which allowed analysis of differences and homologies between the three groups of phi29-like phages, which is included in this review.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 22 February 2018
                Publication date Collection: February 2018
                Volume: 6
                Issue: 8
                Electronic Location Identifier: e00008-18
                Affiliations
                [a ]Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
                [b ]Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
                Author notes
                Address correspondence to Rolf Daniel, rdaniel@ 123456gwdg.de .
                Author information
                https://orcid.org/0000-0002-8646-7925
                Article
                Publisher ID: genomeA00008-18
                DOI: 10.1128/genomeA.00008-18
                PMC ID: 5823994
                PubMed ID: 29472321
                SO-VID: 10c31edd-5089-43ab-82f5-a3ffade97eef
                Copyright © Copyright © 2018 Schilling et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 4 January 2018
                Date accepted : 1 February 2018
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 12, Pages: 2, Words: 1152
                Categories
                Subject: Viruses
                Custom metadata
                cover-date February 2018

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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