Phage JB25 isolate:JB25 | breed:Siphoviridae
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ABSTRACT:
PROVIDER: PRJNA369185 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Phage Genome sequencing and assembly
| PRJNA992180 | ENA
Project description:Here, we report the genome sequence of a Siphoviridae phage named vB_SauS_BaqSau1 (BaqSau1), infecting Staphylococcus aureus Phage BaqSau1 was isolated from a sewage water treatment plant in Sahagún, Córdoba, Colombia. It has a double-stranded DNA (dsDNA) genome of 44,384 bp with 67 predicted genes, including a lysin containing a CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain.
| S-EPMC7155953 | biostudies-literature
Project description:The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10-4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10-3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.
| S-EPMC5913663 | biostudies-literature
Project description:The Bacillus cereus group of bacteria includes, inter alia, the species known to be associated with human diseases and food poisoning. Here, we describe the Bacillus phage vB_BtS_B83 (abbreviated as B83) infecting the species of this group. Transmission electron microscopy (TEM) micrographs indicate that B83 belongs to the Siphoviridae family. B83 is a temperate phage using an arbitrium system for the regulation of the lysis-lysogeny switch, and is probably capable of forming a circular plasmid prophage. Comparative analysis shows that it has been previously sequenced, but was mistaken for a plasmid. B83 shares common genome organization and >46% of proteins with other the Bacillus phage, BMBtp14. Phylograms constructed using large terminase subunits and a pan-genome presence-absence matrix show that these phages form a clade distinct from the closest viruses. Based on the above, we propose the creation of a new genus named Bembunaquatrovirus that includes B83 and BMBtp14.
| S-EPMC6669507 | biostudies-literature
Project description:Background: The Malnad Gidda are unique dwarf Bos indicus cattle native to heavy rainfall Malnad and coastal areas of Karnataka in India. These cattle are highly adapted to harsh climatic conditions and are more resistant to Foot and Mouth disease as compared to other breeds of B.indicus. Since the first genome reference became available from B.taurus Hereford breed, only a few other breeds have been genotyped using high-throughput platforms. Also despite the known reports on high diversity within indicine breeds as compared to taurine breeds, only one draft genome of Nellore and horn transcriptome of Kankrej breed were sequenced at base level resolution. Because of the special characteristics Malnad Gidda possess, it becomes the choice of breed among many indicine cows to study at molecular level and genotyping. Results: Sequencing mRNA from the PBMCs isolated from blood of one selected Malnad Gidda bull resulted in generation of 55 million paired-end reads of 100bp length. Raw sequencing data is processed to trim the adaptor and low quality bases, and are aligned against the whole genome and transcript assemblies of Bos taurus UMD 3.1 and Bos indicus (Nellore breed) respectively. About 72% of the sequenced reads from our study could be mapped against the B.taurus genome where as only 41% of reads could be mapped against the Bos indicus transcript assembly. Transcript assembly from the alignment carried out against the annotated B.taurus UMD 3.1 genome resulted in identification of ~10,000 genes with significant expression (FPKM>1). In a similar analysis against the B.indicus Kankrej assembled transcripts we could identify only ~6,000 transcripts. From the variant analysis of the sequencing data we found ~10,000 SNPs in coding regions among which ~9,000 are novel and ~6,400 are amino acid changing. Conclusions: For the first time we have genotyped and explored the transcriptome of B.indicus Malnad Gidda breed. A comparative analysis of mapping the RNA-Seq data against the available reference genome and transcript sequences is demonstrated. An enhanced utility of transcript sequencing could be achieved by improving or completing the sequence assembly of any B.indicus breed to better characterize the indicine breeds for productivity features and selective breeding.
2016-12-31 | GSE71182 | GEO
Project description:Multidrug-resistant Klebsiella pneumoniae is a nosocomial pathogen, produces septicemia, pneumonia and UTI. Excessive use of antibiotics contributes towards emergence of multidrug-resistance. Bacteriophage-therapy is a potential substitute of antibiotics with many advantages. In this investigation, microbiological and genome characterization of TSK1 bacteriophage and its biofilm elimination capability are presented. TSK1 showed narrow host range and highest stability at pH 7 and 37 °C. TSK1 reduced the growth of K. pneumoniae during the initial 14 hours of infection. Post-treatment with TSK1 against different age K. pneumoniae biofilms reduced 85-100% biomass. Pre-treatment of TSK1 bacteriophage against the biofilm of Klebsiella pneumoniae reduced > 99% biomass in initial 24 hr of incubation. The genome of TSK1 phage comprised 49,836 base pairs with GC composition of 50.44%. Total seventy-five open reading frames (ORFs) were predicted, 25 showed homology with known functional proteins, while 50 were called hypothetical, as no homologs with proved function exists in the genome databases. Blast and phylogenetic analysis put it in the Kp36 virus genus of family Siphoviridae. Proposed packaging strategy of TSK1 bacteriophage genome is headful packaging using the pac sites. The potential of TSK1 bacteriophage could be used to reduce the bacterial load and biofilm in clinical and non-clinical settings.
| S-EPMC6297243 | biostudies-literature
Project description:Genome Sequencing of Rhodococcus bacteriophage
| PRJDB19652 | ENA
Project description:During the fermentation process, Bacillus thuringiensis (Bt) phages can result in bacterial death and decreased yield. In this work, we describe the genome of a new phage related to the Siphoviridae viral family from a Brazilian strain of Bt which showed high nucleotide sequence identity to the genomes of phages phi4l1 and BtCS33.
| S-EPMC5981044 | biostudies-literature
Project description:Bacteriophages are considered to be the most abundant biological entities on the planet. The Siphoviridae are the most commonly encountered tailed phages and contain double-stranded DNA with an average genome size of ∼50 kb. This paper describes the isolation from four different activated sludge plants of the phage RRH1, which is polyvalent, lysing five Rhodococcus species. It has a capsid diameter of only ∼43 nm. Whole-genome sequencing of RRH1 revealed a novel circularly permuted DNA sequence (14,270 bp) carrying 20 putative open reading frames. The genome has a modular arrangement, as reported for those of most Siphoviridae phages, but appears to encode only structural proteins and carry a single lysis gene. All genes are transcribed in the same direction. RRH1 has the smallest genome yet of any described functional Siphoviridae phage. We demonstrate that lytic phage can be recovered from transforming naked DNA into its host bacterium, thus making it a potentially useful model for studying gene function in phages.
| S-EPMC3255915 | biostudies-literature
Project description:Viruses Caudovirales Siphoviridae Guernseyvirinae Jerseyvirus Salmonella phage vB_SenS-EnJE6 Genome sequencing
| PRJNA560145 | ENA