Comparing thousands of circular genomes using the CGView Comparison Tool

Grant, Jason R.; Arantes, Adriano S.; Stothard, Paul

doi:10.1186/1471-2164-13-202

Cited by 269 publications

(207 citation statements)

References 10 publications

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“…The genomic organization and annotation of the seven previously reported ViI-like enterobacterial bacteriophages (26) were used to determine the location of ORF1 in MAM1. The CGView comparison tool (27) was employed to visualize the MAM1 genome and to generate Fig. 3.…”

Section: Methodsmentioning

confidence: 99%

Bacteriophage ϕMAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

Matilla

Salmond

2014

Appl Environ Microbiol

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Members of the enterobacterial genus Serratia are ecologically widespread, and some strains are opportunistic human pathogens. Bacteriophage MAM1 was isolated on Serratia plymuthica A153, a biocontrol rhizosphere strain that produces the potently bioactive antifungal and anticancer haterumalide oocydin A. The MAM1 phage is a generalized transducing phage that infects multiple environmental and clinical isolates of Serratia spp. and a rhizosphere strain of Kluyvera cryocrescens. Electron microscopy allowed classification of MAM1 in the family Myoviridae. Bacteriophage MAM1 is virulent, uses capsular polysaccharides as a receptor, and can transduce chromosomal markers at frequencies of up to 7 ؋ 10 ؊6 transductants per PFU. We also demonstrated transduction of the complete 77-kb oocydin A gene cluster and heterogeneric transduction of a plasmid carrying a type III toxin-antitoxin system. These results support the notion of the potential ecological importance of transducing phages in the acquisition of genes by horizontal gene transfer. Phylogenetic analyses grouped MAM1 within the ViI-like bacteriophages, and genomic analyses revealed that the major differences between MAM1 and other ViI-like phages arise in a region encoding the host recognition determinants. Our results predict that the wider genus of ViI-like phages could be efficient transducing phages, and this possibility has obvious implications for the ecology of horizontal gene transfer, bacterial functional genomics, and synthetic biology.

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Section: Methodsmentioning

confidence: 99%

Bacteriophage ϕMAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

Matilla

Salmond

2014

Appl Environ Microbiol

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“…[10][11][12] were reported by the same research group [28], and contained two complicated inversions. One was nested between 3 and 7 o'clock direction and between 4 and 6 o'clock direction.…”

Section: Three Types Of Genome Rearrangements In H Pylorimentioning

confidence: 99%

“…Several visualizers have been proposed to date [10][11][12][13], but our approach is unique in that we do not presuppose binary comparison between genomes. Comparison against a single reference implicitly assumes the perfection of the reference data.…”

Section: Introductionmentioning

confidence: 99%

Visualization of consensus genome structure without using a reference genome

2017

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Background: Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated.

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“…The linear mimivirus genome is depicted as a circle starting from the site indicated by an arrow. The figure was constructed with the CGView Comparison Tool (CCT) (46). tions revealed that a substantial reduction of their genome specifically occurred at the edges of the genome (35).…”

Section: Figmentioning

confidence: 99%

Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

Fridmann-Sirkis

Milrot

Mutsafi

et al. 2016

J Virol

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The recent discovery of multiple giant double-stranded DNA (dsDNA) viruses blurred the consensual distinction between viruses and cells due to their size, as well as to their structural and genetic complexity. A dramatic feature revealed by these viruses as well as by many positive-strand RNA viruses is their ability to rapidly form elaborate intracellular organelles, termed "viral factories," where viral progeny are continuously generated. Here we report the first isolation of viral factories at progressive postinfection time points. The isolated factories were subjected to mass spectrometry-based proteomics, bioinformatics, and imaging analyses. These analyses revealed that numerous viral proteins are present in the factories but not in mature virions, thus implying that multiple and diverse proteins are required to promote the efficiency of viral factories as "production lines" of viral progeny. Moreover, our results highlight the dynamic and highly complex nature of viral factories, provide new and general insights into viral infection, and substantiate the intriguing notion that viral factories may represent the living state of viruses. IMPORTANCELarge dsDNA viruses such as vaccinia virus and the giant mimivirus, as well as many positive-strand RNA viruses, generate elaborate cytoplasmic organelles in which the multiple and diverse transactions required for viral replication and assembly occur. These organelles, which were termed "viral factories," are attracting much interest due to the increasing realization that the rapid and continuous production of viral progeny is a direct outcome of the elaborate structure and composition of the factories, which act as efficient production lines. To get new insights into the nature and function of viral factories, we devised a method that allows, for the first time, the isolation of these organelles. Analyses of the isolated factories generated at different times postinfection by mass spectrometry-based proteomics provide new perceptions of their role and reveal the highly dynamic nature of these organelles.A n exciting recent development in cellular biology is the realization that intracellular organelles previously considered to be randomly organized are in fact exquisitely ordered and that this order crucially affects their function. A prominent example is provided by replication cycles of positive-strand RNA [(ϩ)RNA] viruses, which were shown to involve massive reorganization of the host cytoskeleton and membrane networks into well-defined cytoplasmic platforms, termed "viral factories" (VFs), within which genome replication and virion assembly are effectively coordinated (1-4). An additional example of highly ordered virus-generated intracellular organelles is the replication cycle of nucleocytoplasmic large DNA viruses (NCLDVs), which include Poxviridae, Phycodnaviridae, Iridoviridae, Asfarviridae, Mimiviridae, and Marseilleviridae (5-7). Specifically, these viruses were shown to partially or exclusively replicate within large and elaborate cytoplasmic ...

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Comparing thousands of circular genomes using the CGView Comparison Tool

Cited by 269 publications

References 10 publications

Bacteriophage ϕMAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

Bacteriophage ϕMAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

Visualization of consensus genome structure without using a reference genome

Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories

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