A, B. Pham circles for phams 3687 (A) and 6944 (B). Phage names are organized by cluster/subcluster sequentially in a clockwise direction around the edge of the circle. Phages containing a gene within each pham are connected by an arc in blue (BLASTP) or red (ClustalW). Cirlces were drawn using Phamerator and thresholds of 32% identity and an E value of 10-50 for ClustalW and BlastP respectively. C, D. Phylogenetic trees of pham 3687 genes (C) and pham 6944 genes (D). Trees were generated using ClustalW multisequence alignments and neighbor-joining. Trees were drawn using NJPlot. Phages are color coded to designate cluster assignment, as shown in the key.

A, B. Pham circles for phams 3687 (A) and 6944 (B). Phage names are organized by cluster/subcluster sequentially in a clockwise direction around the edge of the circle. Phages containing a gene within each pham are connected by an arc in blue (BLASTP) or red (ClustalW). Cirlces were drawn using Phamerator and thresholds of 32% identity and an E value of 10-50 for ClustalW and BlastP respectively. C, D. Phylogenetic trees of pham 3687 genes (C) and pham 6944 genes (D). Trees were generated using ClustalW multisequence alignments and neighbor-joining. Trees were drawn using NJPlot. Phages are color coded to designate cluster assignment, as shown in the key.

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Article
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Bacteriophages isolated on Mycobacterium smegmatis mc(2)155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Clus...

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... Cluster BI phages have linear genomes ranging from 43,060 to 57,623 bp, encompassing from 55 to 91 protein coding genes and no predicted tRNA genes. Comparative analysis of these bacteriophage genomes ( Figure 1) reveals nucleotide sequence conservation to be predominant only in the virion structure and assembly genes module, which presents a genetic arrangement consistent with that observed in other Siphoviridae, such as PhagesDB cluster J mycobacteriophages (Pope et al. 2013;Lopes et al. 2014). Within this module, the terminase gene shows the highest degree of sequence conservation, followed by segments of the portal, capsid maturation and tape measure protein coding genes ( Figure 1). ...
Article
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... The CRISPR interference (CRISPRi) approach was also efficiently used to repress the expression of target genes in the M. tuberculosis complex [80], highlighting the potential application of CRISPR-Cas systems for mycobacteriophage engineering. Moreover, BRED was unsuccessful in the recovery of Omega engineered phage [81] probably since capsid-enclosed proteins maybe are required for recircularization of the phage DNA, indicating that BRED approach might not suitable for all mycobacteriophages. To the best of our knowledge, there is no report yet regarding the application of CRISPR-Cas systems for mycobacteriophage engineering. ...
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... In contrast, the larger siphoviral genomes (e.g., Microbacterium phage PauloDiaboli, 192 kbp) have a large number of nonstructural genes, most of which are of unknown function. Indeed, the main difference between small and large genomes of the siphoviruses is the number of these nonvirion structure and assembly genes (50). Overall, only ~30% of the phage genes have assigned functions. ...
Article
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... Homing endonucleases can be found associated with these elements or simply exist as free-standing genes [30]. A significant number of homing endonucleases have been characterized among phages with recognition sites that lie within genes related to DNA replication and metabolism [31], but they have also been identified to target genes related to virion structure [32,33]. ...
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... Salz was classified as a cluster A phage, the largest cluster (14), and further categorized into subcluster A11. Cluster A phages are similar in size and genomic organization and share a homologous immunity system (15,16). ...
... Darionha was classified as a cluster G phage. Subcluster G1 phages are distinct and unique from other cluster G phages based on a centrally located immunity cassette (integrase and repressor) required for integration-dependent immunity (14,17). For Darionha, the integrase and repressor are located next to each other on genes 32 and 33, respectively. ...
... For Darionha, the integrase and repressor are located next to each other on genes 32 and 33, respectively. These two genes are what define and give the phage its lysogenic properties and its prophage stability (14). Lysogeny was confirmed through the plaque morphology of a characteristic incomplete clearing of the bacterial host. ...
Article
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Mycobacteriophages Darionha, Salz, and ThreeRngTarjay are mycobacteriophages isolated using the host Mycobacterium smegmatis mc ² 155. Following isolation from soil samples, all three siphoviridae phages were characterized, and their genomes were sequenced and annotated.
... In the last few years, our group has characterized and sequenced several Siphoviridae Comparative analysis of these bacteriophage genomes ( Figure 1) reveals nucleotide sequence conservation to be predominant only in the virion structure and assembly genes module, which presents a genetic arrangement consistent with that observed in other Siphoviridae [21]. Within this module, the terminase gene shows the highest degree of sequence conservation, followed by segments of the portal, capsid maturation and tape measure protein coding genes ( Figure 1). ...
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A bstract Bacteriophages typically infect a small set of related bacterial strains. The transfer of bacteriophages between more distant clades of bacteria has often been postulated, but remains mostly unaddressed. In this work we leverage the sequencing of a novel cluster of phages infecting Streptomyces bacteria and the availability of large numbers of complete phage genomes in public repositories to address this question. Using phylogenetic and comparative genomics methods, we show that several clusters of Actinobacteria-infecting phages are more closely related between them, and with a small group of Firmicutes phages, than with any other actinobacteriophage lineage. These data indicate that this heterogeneous group of phages shares a common ancestor with well-defined genome structure. Analysis of genomic %GC content and codon usage bias shows that these actinobacteriophages are poorly adapted to their Actinobacteria hosts, suggesting that this phage lineage could have originated in an ancestor of the Firmicutes, adapted to the high %GC content members of this phylum, and later migrated to the Actinobacteria, or that selective pressure for enhanced translational throughput is significantly lower for phages infecting Actinobacteria hosts.
... There is an IS110-like element in phage Omega and some other Cluster J phages (52), IS605-like elements in phage Llij and several other Subcluster F1 phages -although inserted at several distinct locations -an IS1096-like element in the Cluster G phage LouisV14, and an IS1380-like element in Guillsminger (Subcluster K5). There are instances of introns (e.g. in Omega and other Cluster J phages) (52), and inteins, especially in terminase large subunit genes (65). However, there are a greater number of genes appearing to code for stand-alone homing endonucleases or HNH proteins (65). ...
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... Thus bioinformatics holds significant importance in countless disciplines of biotechnology such as comparative genomics, drug designing, proteomics, molecular modelling, microbial genomics etc GENEVA Categorizes segmentally altered genes in many complete microbial genomes [79] HuGE Index Human tissues gene expression database [80] Inverted Repeats Finder Find inverted repeats in genomic DNA [81] ORChID Database stores hydroxyl radical cleavage data of DNA sequences [82] Operons Predicts functional gene clusters [83] Optimus Retrieve conserved gene cluster data from numerous microbial genomes [84] Predictome Visualizing tool for bio complexes [85] Tandem Repeat Database Store information on tandem repeats in genomic DNA [86] VisANT Tools for visualizing and analysing many biological interactions [87] BSG Identification of transcription factor binding sites [88] TFSVM Detection of transcription factor binding site [89] symposium on biotechnology and bioinformatics. In [93] Phyre and Phyre2 Tool for protein structure prediction [94] HMMSTR For the prediction of sequence-structure correlations in proteins [95] MODELLER Predicts 3D structure of protein [96] JPRED/ APSSP2 Predicts secondary structures of proteins [97] RaptorX Predicts protein structure [98] PHD Predicts neural network structure [99] Freely Evolutionary computation in bioinformatics. ...
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... Seventeen bacteriophages of Gordonia have been isolated, sequenced, and deposited in GenBank (5)(6)(7)(8)(9). It is unclear if the phages' genomic relationships reflect those of other phages of the phylum Actinobacteria, notably those of Mycobacterium smegmatis mc 2 155 whose phages exhibit a continuum of genetic diversity (10)(11)(12)(13)(14)(15)(16). The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program is a course-based research experience in which undergraduates are immersed in research, using phage isolation and bioinformatics as a method to fuse authentic research and education (17). ...
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... The expression of a repressor, of an excise, or of a Crolike protein would need to be regulated in order to control phage lifecycles. In many other phages (45,49), the gene in the corresponding location as Ukulele gp53 encodes a DNA binding protein and is the putative repressor. This gene would also need to have its transcription controlled, but Ukulele gp53 does not have repressor characteristics. ...
Article
Mycobacteriophages (phages) are diverse and abundant viruses that infect species of the genus Mycobacterium. Mycobacteriophages are categorized into clusters based primarily on nucleotide similarity (18). Some clusters are well-characterized, while others, such as Cluster E, are poorly characterized (20). There are 54 members of Cluster E (39) including the phage Ukulele that was isolated at the University of Maine in 2011. This thesis is aimed towards characterizing Cluster E phages using Ukulele as a model. Cluster E phages have long tails of approximately 300 nm and they produce slightly turbid plaques on a lawn of Mycobacterium smegmatis. Putative simple terminators and two repeat sequences potentially involved in regulating gene transcription or translation were identified, as well as an HNH endonuclease at the right end of the genome that may functionally associate with the terminase. Cluster E phages are temperate but genes that encode the repressor and excise are not obvious. Gp88 was identified as a potential repressor gene and gp52 was identified as a potential excise, repressor, or Cro-like gene. Each of these genes was deleted independently from the Ukulele genome using the Bacteriophage Recombineering of Electroporated DNA system (35) to learn more about its function. Gp88Δ mutants are not viable and have not yet been isolated using complementation. Therefore, gp88 does not encode the repressor. Gp52Δ mutants have been detected but a pure mutant has not yet been isolated and further experiments are needed to determine the function of gp52.