scholarly journals Complete Circular Genome Sequences of Brachyspira hyodysenteriae Isolates of the Four Different Sequence Types Causing Swine Dysentery in Switzerland

2021 ◽  
Vol 10 (39) ◽  
Author(s):  
Ana B. García-Martín ◽  
Sarah Schmitt ◽  
Friederike Zeeh ◽  
Vincent Perreten
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Hybrid Assembly ◽  
Swine Dysentery ◽  
Content Type ◽  
Brachyspira Hyodysenteriae ◽  
Oxford Nanopore ◽  
Sequencing Platforms ◽  
Sequence Types ◽  
Oxford Nanopore Technologies

The complete genomes of four Brachyspira hyodysenteriae isolates of the four different sequence types (STs) (ST6, ST66, ST196, and ST197) causing swine dysentery in Switzerland were generated by whole-genome sequencing and de novo hybrid assembly of reads obtained from second (Illumina) and third (Oxford Nanopore Technologies and Pacific Biosciences) high-throughput sequencing platforms.

scholarly journals The Levels of Brachyspira hyodysenteriae Binding to Porcine Colonic Mucins Differ between Individuals, and Binding Is Increased to Mucins from Infected Pigs withDe NovoMUC5AC Synthesis

2015 ◽  
Vol 83 (4) ◽  
pp. 1610-1619 ◽  
Author(s):  
Macarena P. Quintana-Hayashi ◽  
Maxime Mahu ◽  
Nele De Pauw ◽  
Filip Boyen ◽  
Frank Pasmans ◽  
...  
Keyword(s):  
Binding Sites ◽  
De Novo ◽  
Density Gradient Centrifugation ◽  
Gradient Centrifugation ◽  
Antibody Detection ◽  
Swine Dysentery ◽  
Content Type ◽  
Brachyspira Hyodysenteriae ◽  
Main Component ◽  
And Control

Brachyspira hyodysenteriaecolonizes the pig colon, resulting in mucohemorrhagic diarrhea and growth retardation. Fecal mucus is a characteristic feature of swine dysentery; therefore, we investigated how the mucin environment changes in the colon during infection withB. hyodysenteriaeand how these changes affect this bacterium's interaction with mucins. We isolated and characterized mucins, the main component of mucus, from the colon of experimentally inoculated and control pigs and investigatedB. hyodysenteriaebinding to these mucins. Fluorescence microscopy revealed a massive mucus induction and disorganized mucus structure in the colon of pigs with swine dysentery. Quantitative PCR (qPCR) and antibody detection demonstrated that the mucus composition of pigs with swine dysentery was characterized byde novoexpression of MUC5AC and increased expression of MUC2 in the colon. Mucins from the colon of inoculated and control pigs were isolated by two steps of isopycnic density gradient centrifugation. The mucin densities of control and inoculated pigs were similar, whereas the mucin quantity was 5-fold higher during infection. The level ofB. hyodysenteriaebinding to mucins differed between pigs, and there was increased binding to soluble mucins isolated from pigs with swine dysentery. The ability ofB. hyodysenteriaeto bind, measured in relation to the total mucin contents of mucus in sick versus healthy pigs, increased 7-fold during infection. Together, the results indicate thatB. hyodysenteriaebinds to carbohydrate structures on the mucins as these differ between individuals. Furthermore,B. hyodysenteriaeinfection induces changes to the mucus niche which substantially increase the amount ofB. hyodysenteriaebinding sites in the mucus.

scholarly journals Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Kristian Jensen ◽  
Kosai Al-Nakeeb ◽  
Anna Koza ◽  
Ahmad A. Zeidan
Keyword(s):  
Genome Sequence ◽  
Probiotic Bacterium ◽  
Content Type ◽  
Short Read Sequencing ◽  
Bifidobacterium Animalis ◽  
Oxford Nanopore ◽  
Hybrid Genome ◽  
Long Read ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies long-read and Illumina short-read sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 containing 1,944,152 bp, with a G+C content of 60.5% and 1,615 genes.

scholarly journals Complete Closed Genome Sequence of the Inulin-Utilizing Lactiplantibacillus plantarum Strain Lp900, Obtained Using a Hybrid Nanopore and Illumina Assembly

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Jori Fuhren ◽  
Reindert Nijland ◽  
Michiel Wels ◽  
Jos Boekhorst ◽  
Michiel Kleerebezem
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Dna Sequence ◽  
Genome Sequence ◽  
De Novo ◽  
Circular Chromosome ◽  
Content Type ◽  
Diverse Species ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Lactiplantibacillus plantarum is a genetically and phenotypically diverse species of lactic acid bacteria. We announce the hybrid de novo assembly of Oxford Nanopore Technologies and Illumina DNA sequence reads, producing a closed circular chromosome of 3,206,992 bp and six plasmids of the inulin-utilizing L. plantarum strain Lp900.

scholarly journals De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

2020 ◽  
Vol 10 (8) ◽  
pp. 2585-2592
Author(s):  
Sam D. Heraghty ◽  
John M. Sutton ◽  
Meaghan L. Pimsler ◽  
Janna L. Fierst ◽  
James P. Strange ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Bombus Terrestris ◽  
Bumble Bee ◽  
Hybrid Assembly ◽  
Widespread Species ◽  
Oxford Nanopore ◽  
Genome Assemblies ◽  
High Degree ◽  
Oxford Nanopore Technologies

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

scholarly journals Real-Time Sequencing of Mycobacterium tuberculosis: Are We There Yet?

2017 ◽  
Vol 55 (5) ◽  
pp. 1249-1254 ◽  
Author(s):  
Robyn S. Lee ◽  
Madhukar Pai
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Real Time ◽  
Phylogenetic Trees ◽  
Illumina Miseq ◽  
Turnaround Time ◽  
Epidemiologic Studies ◽  
Content Type ◽  
Leading Role ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Whole-genome sequencing has taken a leading role in epidemiologic studies of tuberculosis, but thus far, its real-time clinical utility has been low, in part because of the requirement for culture. In their report in this issue, Votintseva et al. (A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. A. Peto, D. W. Crook, and Z. Iqbal, J Clin Microbiol 55:1285–1298, 2017, https://doi.org/10.1128/JCM.02483-16 ) present a new method for extracting Mycobacterium tuberculosis DNA directly from smear-positive respiratory samples, making it feasible to generate drug resistance predictions and phylogenetic trees in 44 h with the Illumina MiSeq. They also illustrate the potential for a <24-h turnaround time from DNA extraction to clinically relevant results with Illumina MiniSeq and Oxford Nanopore Technologies MinION. We comment on the promise and limitations of these approaches.

scholarly journals Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms

2020 ◽  
Vol 9 (32) ◽  
Author(s):  
Sohaib Sarfraz ◽  
Saïd Oulghazi ◽  
Jérémy Cigna ◽  
Shahbaz Talib Sahi ◽  
Kashif Riaz ◽  
...  
Keyword(s):  
Complete Genome ◽  
Type Strain ◽  
Gc Content ◽  
Illumina Miseq ◽  
Blackleg Disease ◽  
Circular Chromosome ◽  
Content Type ◽  
Potato Plants ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

ABSTRACT Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

scholarly journals A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

2018 ◽  
Author(s):  
Stáphane Deschamps ◽  
Yun Zhang ◽  
Victor Llaca ◽  
Liang Ye ◽  
Gregory May ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
De Novo ◽  
Hybrid Assembly ◽  
The Public ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Optical Maps ◽  
Eukaryotic Genomes ◽  
Direct Label

The advent of long-read sequencing technologies has greatly facilitated assemblies of large eukaryotic genomes. In this paper, Oxford Nanopore sequences generated on a MinION sequencer were combined with BioNano Genomics Direct Label and Stain (DLS) optical maps to generate a chromosome-scale de novo assembly of the repeat-rich Sorghum bicolor Tx430 genome. The final hybrid assembly consists of 29 scaffolds, encompassing in most cases entire chromosome arms. It has a scaffold N50 value of 33.28Mbps and covers >90% of Sorghum bicolor expected genome length. A sequence accuracy of 99.67% was obtained in unique regions after aligning contigs against Illumina Tx430 data. Alignments showed that 99.4% of the 34,211 public gene models are present in the assembly, including 94.2% mapping end-to-end. Comparisons of the DLS optical maps against the public Sorghum Bicolor v3.0.1 BTx623 genome assembly suggest the presence of substantial genomic rearrangements whose origin remains to be determined.

scholarly journals Methplotlib: analysis of modified nucleotides from nanopore sequencing

2019 ◽  
Author(s):  
Wouter De Coster ◽  
Mojca Strazisar
Keyword(s):  
Gene Expression Regulation ◽  
Command Line ◽  
Nanopore Sequencing ◽  
Modified Nucleotides ◽  
Oxford Nanopore ◽  
Command Line Tool ◽  
Within Subjects ◽  
Allele Specific ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

AbstractSummaryModified nucleotides play a crucial role in gene expression regulation. Here we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele specific modification within subjects and differential modification frequency across subjects.Availability and implementationThe methplotlib command-line tool is written in Python3, is compatible with Linux, Mac OS and the MS Windows 10 Subsystem for Linux and released under the MIT license. The source code can be found at https://github.com/wdecoster/methplotlib and can be installed from PyPI and bioconda. Our repository includes test data and the tool is continuously tested at [email protected]

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