Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete Genome Sequences of Three Novel Pseudomonas fluorescens SBW25 Bacteriophages, Noxifer, Phabio, and Skulduggery.

ABSTRACT: Three novel bacteriophages, two of which are jumbophages, were isolated from compost in Auckland, New Zealand. Noxifer, Phabio, and Skulduggery are double-stranded DNA (dsDNA) phages with genome sizes of 278,136 bp (Noxifer), 309,157 bp (Phabio), and 62,978 bp (Skulduggery).

SUBMITTER: Wojtus JK

PROVIDER: S-EPMC5543642 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete Genome Sequences of Three Novel <i>Pseudomonas fluorescens</i> SBW25 Bacteriophages, Noxifer, Phabio, and Skulduggery.

Wojtus Joanna K JK Fitch Jess L JL Christian Eli E Dalefield Tara T Lawes Jacob K JK Kumar Kirtana K Peebles Craig L CL Altermann Eric E Hendrickson Heather L HL

Genome announcements 20170803 31

Three novel bacteriophages, two of which are jumbophages, were isolated from compost in Auckland, New Zealand. Noxifer, Phabio, and Skulduggery are double-stranded DNA (dsDNA) phages with genome sizes of 278,136 bp (Noxifer), 309,157 bp (Phabio), and 62,978 bp (Skulduggery). ...[more]

PMID: 28774980

Similar Datasets

Genome Update for Pseudomonas fluorescens Isolate SBW25.

Project description:We report a genome update for Pseudomonas fluorescens isolate SBW25. The updated genome assembly, which was derived from the original isolate, is based on PacBio long-read sequence data. It shows three minor differences, compared with the previously published genome sequence. Original annotations were merged with recent automated annotations to preserve information.

| S-EPMC9933645 | biostudies-literature

Complete Genome Sequences of Pseudomonas fluorescens Bacteriophages Isolated from Freshwater Samples in Omaha, Nebraska.

Project description:The complete genome sequences of four Pseudomonas fluorescens bacteriophages, UNO-SLW1 to UNO-SLW4, isolated from freshwater samples, are 39,092 to 39,215 bp long. The genomes are highly similar (identity, >0.995) but dissimilar from that of Pseudomonas phage Pf-10 (the closest relative, 0.685 to 0.686 identity), with 48 to 49 protein-coding genes and 66 regulatory sites predicted.

| S-EPMC5364227 | biostudies-literature

Barcoding Populations of Pseudomonas fluorescens SBW25.

Project description:In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.

| S-EPMC10275814 | biostudies-literature

Complete Genome Sequences of Three Bacillus anthracis Bacteriophages.

Project description:The new highly effective Bacillus anthracis phages Negev_SA, Carmel_SA, and Tavor_SA were isolated from soil samples, and their complete genomes were sequenced and analyzed. The isolated phages have potential use in future phage therapy treatment against anthrax.

| S-EPMC5754477 | biostudies-literature

Complete genome sequences of two novel autographiviruses infecting a bacterium from the Pseudomonas fluorescens group.

Project description:In this paper, we describe two independent isolates of a new member of the subfamily Autographivirinae, Pseudomonas phage KNP. The type strain (KNP) has a linear, 40,491-bp-long genome with GC content of 57.3%, and 50 coding DNA sequences (CDSs). The genome of the second strain (WRT) contains one CDS less, encodes a significantly different tail fiber protein and is shorter (40,214 bp; GC content, 57.4%). Phylogenetic analysis indicates that both KNP and WRT belong to the genus T7virus. Together with genetically similar Pseudomonas phages (gh-1, phiPSA2, phiPsa17, PPPL-1, shl2, phi15, PPpW-4, UNO-SLW4, phiIBB-PF7A, Pf-10, and Phi-S1), they form a divergent yet coherent group that stands apart from the T7-like viruses (sensu lato). Analysis of the diversity of this group and its relatedness to other members of the subfamily Autographivirinae led us to the conclusion that this group might be considered as a candidate for a new genus.

| S-EPMC5563517 | biostudies-literature

Genome Sequences of Three Novel Bacillus cereus Bacteriophages.

Project description:The Bacillus cereus group is an assemblage of highly related firmicute bacteria that cause a variety of diseases in animals, including insects and humans. We announce three high-quality, complete genome sequences of bacteriophages we isolated from soil samples taken at the bases of fruit trees in Utah County, Utah. While two of the phages (Shanette and JL) are highly related myoviruses, the bacteriophage Basilisk is a siphovirus.

| S-EPMC3900887 | biostudies-literature

Complete Genome Sequences of Three Siphoviridae Bacteriophages Infecting Salmonella enterica Serovar Enteritidis.

Project description:Three bacteriophages, 118970_sal1, 118970_sal2, and 64795_sal3, were isolated from water buffalo feces in southern Italy, exhibiting lytic activity against Salmonella enterica serovar Enteritidis. These bacteriophages belong to the Siphoviridae family and have a 60,113-bp, 123,930-bp, and 48,094-bp double-stranded DNA (dsDNA) genome containing 72, 173, and 80 coding sequences (CDSs), respectively.

| S-EPMC5114364 | biostudies-literature

Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25.

Project description:Repeated evolution of functionally similar phenotypes is observed throughout the tree of life. The extent to which the underlying genetics are conserved remains an area of considerable interest. Previously, we reported the evolution of colony switching in two independent lineages of Pseudomonas fluorescens SBW25. The phenotypic and genotypic bases of colony switching in the first lineage (Line 1) have been described elsewhere. Here, we deconstruct the evolution of colony switching in the second lineage (Line 6). We show that, as for Line 1, Line 6 colony switching results from an increase in the expression of a colanic acid-like polymer (CAP). At the genetic level, nine mutations occur in Line 6. Only one of these-a nonsynonymous point mutation in the housekeeping sigma factor rpoD-is required for colony switching. In contrast, the genetic basis of colony switching in Line 1 is a mutation in the metabolic gene carB. A molecular model has recently been proposed whereby the carB mutation increases capsulation by redressing the intracellular balance of positive (ribosomes) and negative (RsmAE/CsrA) regulators of a positive feedback loop in capsule expression. We show that Line 6 colony switching is consistent with this model; the rpoD mutation generates an increase in ribosomal gene expression, and ultimately an increase in CAP expression.

| S-EPMC6519391 | biostudies-literature

Complete Genome Sequences of Broad-Host-Range Pseudomonas aeruginosa Bacteriophages ΦR18 and ΦS12-1.

Project description:Pseudomonas aeruginosa is an important cause of racehorse keratitis. Bacteriophage therapy has the potential to aid in the prevention and treatment of diseases caused by P. aeruginosa We present here the complete genome sequences of two phages, ΦR18 and ΦS12-1, which exhibit infectivity for a broad range of P. aeruginosa isolates.

| S-EPMC4859162 | biostudies-literature

Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25.

Project description:The histidine utilization (hut) locus of Pseudomonas fluorescens SBW25 confers the ability to utilize histidine as a sole carbon and nitrogen source. Genetic analysis using a combination of site-directed mutagenesis and chromosomally integrated lacZ fusions showed the hut locus to be composed of 13 genes organized in 3 transcriptional units: hutF, hutCD, and 10 genes from hutU to hutG (which includes 2 copies of hutH, 1 of which is nonfunctional). Inactivation of hutF eliminated the ability to grow on histidine, indicating that SBW25 degrades histidine by the five-step enzymatic pathway. The 3 hut operons are negatively regulated by the HutC repressor with urocanate (the first intermediate of the histidine degradation pathway) as the physiological inducer. 5'-RACE analysis of transcriptional start sites revealed involvement of both sigma(54) (for the hutU-G operon) and sigma(70) (for hutF); the involvement of sigma(54) was experimentally demonstrated. CbrB (an enhancer binding protein for sigma(54) recruitment) was required for bacterial growth on histidine, indicating positive control of hut gene expression by CbrB. Recognition that a gene (named hutD) encoding a widely distributed conserved hypothetical protein is transcribed along with hutC led to analysis of its role. Mutational and gene fusion studies showed that HutD functions independently of HutC. Growth and fitness assays in laboratory media and on sugar beet seedlings suggest that HutD acts as a governor that sets an upper bound to the level of hut activity.

| S-EPMC1950622 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data