scholarly journals Whole-Genome Sequencing of an Unusual Human Papillomavirus (HPV71) from Latin America (Brazil)

2020 ◽  
Vol 9 (24) ◽  
Author(s):  
Edivaldo Costa Sousa Junior ◽  
Allan Kaio Silva ◽  
Laryssa Danielle da Silva Reis ◽  
Lana Patricia da Silva Fonseca ◽  
Fabiano Reis da Silva ◽  
...  
Keyword(s):  
Latin America ◽  
Human Papillomavirus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Whole Genome ◽  
Complete Genome Sequencing

ABSTRACT We report the complete genome sequencing of human papillomavirus 71 from Latin America (Brazil).

scholarly journals Whole-Genome Sequencing and Annotation of Clostridium tyrobutyricum Strain Cirm BIA 2237, Isolated from Silage

2019 ◽  
Vol 8 (30) ◽  
Author(s):  
Edouard Munier ◽  
Hélène Licandro-Séraut ◽  
Christine Achilleos ◽  
Rémy Cachon ◽  
Eric Beuvier
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Clostridium Tyrobutyricum ◽  
Content Type ◽  
Complete Genome Sequencing

Clostridium tyrobutyricum is the main bacterial species leading to the late blowing defect, a major cause of spoilage in semihard and hard cheeses. This study reports the complete genome sequencing, assembly, and annotation of C. tyrobutyricum strain Cirm BIA 2237, formerly called CNRZ 608, isolated from silage.

scholarly journals Complete Genome Sequencing of Acinetobacter sp. Strain LoGeW2-3, Isolated from the Pellet of a White Stork, Reveals a Novel Class D Beta-Lactamase Gene

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Ulrike Blaschke ◽  
Evelyn Skiebe ◽  
Michael Kaatz ◽  
Paul G. Higgins ◽  
Yvonne Pfeifer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
White Stork ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Ciconia Ciconia ◽  
Complete Genome Sequencing ◽  
Class D ◽  
Lactamase Gene

ABSTRACT Whole-genome sequencing of Acinetobacter sp. strain LoGeW2-3, isolated from the pellet of a white stork (Ciconia ciconia), reveals the presence of a plasmid of 179,399 bp encoding a CRISPR-Cas (clustered regularly interspaced short palindromic repeats and associated genes) system of the I-F type, and the chromosomally encoded novel class D beta-lactamase OXA-568.

scholarly journals Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Jennifer K. Bender ◽  
Stefan Fiedler ◽  
Ingo Klare ◽  
Guido Werner
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Enterococcus Faecium ◽  
Complete Genome ◽  
Laboratory Strain ◽  
Whole Genome ◽  
Coding Sequences

The genome sequence of the commensal and widely used laboratory strain Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding sequences as assigned by NCBI.

scholarly journals Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment

2016 ◽  
Vol 55 (3) ◽  
pp. 811-823 ◽  
Author(s):  
Tengguo Li ◽  
Elizabeth R. Unger ◽  
Dhwani Batra ◽  
Mili Sheth ◽  
Martin Steinau ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Target Enrichment ◽  
Degenerate Primers ◽  
Illumina Hiseq ◽  
Hpv Typing ◽  
Type Assignment ◽  
Hpv Types

ABSTRACTWe designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.

scholarly journals Draft Genome Sequencing of Pseudoalteromonas tetraodonis Strain kknpp56, a Potent Biofilm-Forming Bacterium Isolated from Early-Stage Marine Biofilm

2021 ◽  
Vol 10 (38) ◽  
Author(s):  
Meora Rajeev ◽  
T. J. Sushmitha ◽  
Subba Rao Toleti ◽  
Shunmugiah Karutha Pandian
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Marine Bacterium ◽  
Early Stage ◽  
Draft Genome ◽  
Whole Genome ◽  
Content Type ◽  
Marine Biofilm ◽  
Draft Genome Sequencing

Pseudoalteromonas tetraodonis strain kknpp56 is an exopolysaccharide (EPS)-producing marine bacterium that forms potent biofilm. To determine the biosynthesis pathways involved in the EPS production of this bacterium, whole-genome sequencing was performed. The complete genome comes from one chromosome containing 3.72 Mbp of DNA with a G+C content of 41%.

scholarly journals Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Ainsley C. Nicholson ◽  
Melissa Bell ◽  
Ben W. Humrighouse ◽  
John R. McQuiston
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Relevance ◽  
Complete Genome ◽  
Growth Characteristics ◽  
Clinical Samples ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Gram Positive

Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus “ Lawsonella clevelandensis ” (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing.

scholarly journals Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yasuhiro Uchimura ◽  
Madeleine Wyss ◽  
Sandrine Brugiroux ◽  
Julien P. Limenitakis ◽  
Bärbel Stecher ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
Sequencing Platform ◽  
Germ Free

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

scholarly journals Complete Genome Sequence of Acinetobacter sp. Strain NCu2D-2 Isolated from a Mouse

2017 ◽  
Vol 5 (4) ◽  
Author(s):  
Ulrike Blaschke ◽  
Gottfried Wilharm
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Insertion Sequences ◽  
Whole Genome ◽  
Nosocomial Pathogen ◽  
Content Type

ABSTRACT Whole-genome sequencing of Acinetobacter sp. strain NCu2D-2, isolated from the trachea of a mouse, revealed the presence of a plasmid of 309,964 bp with little overall similarity to known plasmids and enriched in insertion sequences (ISs) closely related to IS elements known from the nosocomial pathogen Acinetobacter baumannii.

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