scholarly journals Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

2018 ◽  
Author(s):  
Madhan R Tirumalai ◽  
Victor G. Stepanov ◽  
Andrea Wünsche ◽  
Saied Montazari ◽  
Racquel O. Gonzalez ◽  
...  
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Health Concern ◽  
Genome Comparison ◽  
Specific Gene ◽  
Planetary Protection ◽  
Genome Variability ◽  
Whole Genome Comparison ◽  
Multiple Strains ◽  
Reading Frames

AbstractBackgroundBacillusstrains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome ofBacillus safensisstrain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome ofB. pumilus SAFR-032, as well as draft genomes ofB. safensisJPL-MERTA-8-2 and the type strainB. pumilusATCC7061T. In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains ofB. pumilusorB. safensis.ResultsThe FO-36b gene order is essentially the same as that in SAFR-032 and otherB. pumilusstrains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061T. The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with theBacillusbacteriophage SPP1 (NC_004166) andBrevibacillusphage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially allsafensis/pumilusstrains. Seven unique genes are part of these phage elements. Comparison ofgyrAsequences from FO-36b, SAFR-032, ATCC7061T, and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups ofB. pumiluswhile the other houses all theB. safensisstrains.ConclusionsIt is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named asB. pumilusactually belong to theB. safensisgroup.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

scholarly journals Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
T. O. C. Faleye ◽  
O. M. Adewumi ◽  
D. Klapsa ◽  
M. Majumdar ◽  
J. Martin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Complete Genome ◽  
Neutralization Assay ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Overlapping Open Reading Frames ◽  
Reading Frames

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

scholarly journals Complete genome sequence of GII.9 norovirus

2021 ◽  
Author(s):  
Zilong Zhang ◽  
Danlei Liu ◽  
Zilei Zhang ◽  
Peng Tian ◽  
Shenwei Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
Open Reading Frames ◽  
Viral Sequence ◽  
Sequence Comparisons ◽  
Rapid Amplification ◽  
Genome Level ◽  
Reading Frames

AbstractNorovirus is recognized as one of the leading causes of acute gastroenteritis outbreaks. Genotype GII.9 was first detected in Norfolk, VA, USA, in 1997. However, the complete genome sequence of this genotype has not yet been determined. In this study, a complete genome sequence of GII.9[P7] norovirus, SCD1878_GII.9[P7], from a patient was determined using high-throughput sequencing and rapid amplification of cDNA ends (RACE) technology. The complete genome sequence of SCD1878_GII.9[P7] is 7544 nucleotides (nt) in length with a 3’ poly(A) tail and contains three open reading frames. Sequence comparisons indicated that SCD1878_GII.9[P7] shares 92.1%-92.3% nucleotide sequence identity with GII.P7 (AB258331 and AB039777) and 96.7%-97.4% identity with GII.9 (AY038599 and DQ379715). The results suggested that SCD1878_GII.9[P7] is a member of P genotype GII.P7 and G genotype GII.9. This viral sequence fills a gap at the whole-genome level for the GII.9 genotype.

scholarly journals Complete Genome Sequence of theBacillus pumilusPhage Leo2

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Sondos Badran ◽  
Nathanael Morales ◽  
Phillip Schick ◽  
Brandon Jacoby ◽  
William Villella ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacillus Pumilus ◽  
Open Reading Frames ◽  
Gram Positive ◽  
Coding Regions ◽  
Symbiotic Interactions ◽  
Associated Functions ◽  
Reading Frames

ABSTRACTBacillusspp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect aBacillus pumilusstrain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.

scholarly journals Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Christine Pourcel ◽  
Cédric Midoux ◽  
Libera Latino ◽  
Marie-Agnès Petit ◽  
Gilles Vergnaud
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Genome Sequences ◽  
Reading Frames

vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A are Pseudomonas aeruginosa bacteriophages belonging, respectively, to the Lit1virus genus of the Podoviridae family and the Pbunavirus genus of the Myoviridae family. Their genomes are 72,778 bp and 65,712 bp long, containing 94 and 93 predicted open reading frames, respectively.

scholarly journals Complete Genome Sequence of a Novel Satellite Virus Associated with Cassava Plants

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
Adriana N. Souza ◽  
Fábio N. Silva ◽  
Claudine M. Carvalho
Keyword(s):  
Amino Acids ◽  
Coat Protein ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Putative Protein ◽  
Satellite Virus ◽  
Cassava Plant ◽  
Reading Frames

ABSTRACT A novel satellite virus of 1,228 bp in length was found in a single cassava plant. Bioinformatic analyses show that it has two open reading frames (ORFs) in its genome, probably encoding a coat protein of 156 and a putative protein of 90 amino acids.

scholarly journals Complete Genome Sequence of a Renamed Isolate, Trichoplusia ni Ascovirus 6b, from the United States

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Yuan-Yuan Liu ◽  
Wen-Fei Xian ◽  
Jin Xue ◽  
Yong-Lu Wei ◽  
Xiao-Wen Cheng ◽  
...  
Keyword(s):  
United States ◽  
Phylogenetic Relationship ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Trichoplusia Ni ◽  
The United States ◽  
Open Reading Frames ◽  
First Time ◽  
Reading Frames

ABSTRACT The complete genome of Trichoplusia ni ascovirus 6b (TnAV-6b) was sequenced for the first time. The TnAV-6b isolate, which has its closest phylogenetic relationship with the TnAV-6a isolate, has a circular genome of 185,664 bp, with a G+C content of 46.0% and 178 predicted open reading frames.

scholarly journals Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Franck Dorkeld ◽  
Réjane Streiff ◽  
Carole Kerdelhué ◽  
Mylène Ogliastro
Keyword(s):  
Complete Genome ◽  
Open Reading Frames ◽  
Thaumetopoea Pityocampa ◽  
Data Sets ◽  
Genome Sequences ◽  
Virus Family ◽  
Content Type ◽  
Pine Processionary Moth ◽  
Transcriptomic Data ◽  
Reading Frames

ABSTRACT The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

scholarly journals Complete Genome Sequence of a Bacteroides fragilis Bacteriophage, vB_BfrS_NCTC

2021 ◽  
Vol 10 (29) ◽  
Author(s):  
Mohammad A. Tariq ◽  
Simon R. Carding
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacteroides Fragilis ◽  
Opportunistic Pathogen ◽  
Open Reading Frames ◽  
Obligate Anaerobe ◽  
Commensal Bacterium ◽  
Content Type ◽  
Reading Frames

Bacteroides fragilis is an obligate anaerobe and a common gut commensal bacterium that is also an important opportunistic pathogen. Here, we present the complete genome sequence of the circularly permuted B. fragilis bacteriophage vB_BfrS_NCTC. It comprises 47,160 bp, with 69 open reading frames.

scholarly journals Complete Genome Sequence of a Rhabdovirus Strain from Culex Mosquitos Collected in Southern Switzerland

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jakub Kubacki ◽  
Isabelle Hardmeier ◽  
Weihong Qi ◽  
Eleonora Flacio ◽  
Mauro Tonolla ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Culex Pipiens ◽  
Full Length ◽  
Open Reading Frames ◽  
Content Type ◽  
Full Length Genome ◽  
Reading Frames

ABSTRACT We report here the full-length genome sequence of a rhabdovirus strain detected in a pool of 21 Culex pipiens and Culex torrentium mosquitos collected in southern Switzerland. The genome has a length of 11,914 nucleotides and encodes five major putative open reading frames.

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