scholarly journals Using shotgun sequence data to find active restriction enzyme genes

2008 ◽  
Vol 37 (1) ◽  
pp. e1-e1 ◽  
Author(s):  
Yu Zheng ◽  
Janos Posfai ◽  
Richard D. Morgan ◽  
Tamas Vincze ◽  
Richard J. Roberts
Keyword(s):  
Restriction Enzyme ◽  
Sequence Data ◽  
Shotgun Sequence ◽  
Active Restriction

scholarly journals Extensive Pericentric Rearrangements in the Bread Wheat ( Triticum aestivum L.) Genotype “Chinese Spring” Revealed from Chromosome Shotgun Sequence Data

2014 ◽  
Vol 6 (11) ◽  
pp. 3039-3048 ◽  
Author(s):  
Jian Ma ◽  
Jiri Stiller ◽  
Yuming Wei ◽  
You-Liang Zheng ◽  
Katrien M. Devos ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Chinese Spring ◽  
Sequence Data ◽  
Triticum Aestivum L ◽  
Shotgun Sequence

scholarly journals Long-read, whole-genome shotgun sequence data for five model organisms

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Kristi E Kim ◽  
Paul Peluso ◽  
Primo Babayan ◽  
P. Jane Yeadon ◽  
Charles Yu ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Shotgun ◽  
Model Organisms ◽  
Whole Genome ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Long Read ◽  
Genome Shotgun Sequence

scholarly journals Comparison of Sequencing of the por Gene and Typing of the opa Gene for Discrimination of Neisseria gonorrhoeae Strains from Sexual Contacts

2000 ◽  
Vol 38 (12) ◽  
pp. 4430-4438 ◽  
Author(s):  
Raphael P. Viscidi ◽  
James C. Demma ◽  
Jing Gu ◽  
Jonathan Zenilman
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Restriction Enzyme ◽  
Sequence Data ◽  
Typing Method ◽  
Laboratory Personnel ◽  
Dna Sequence Data ◽  
Sexual Contacts

Typing of gonococcal strains is a valuable tool for the biological confirmation of sexual contacts. We have developed a typing method based on DNA sequencing of two overlapping por gene fragments generated by a heminested PCR. We compared sequencing of thepor gene (POR sequencing) and typing of the opagene (OPA typing) for the characterization of strains from 17 sexual partnerships. Both methods were highly discriminatory. A different genotype was detected in 15 of the 17 epidemiologically unconnected couples by POR sequencing and in 16 of the 17 couples by OPA typing with restriction enzyme HpaII. Within partnerships, identical genotypes were obtained from 16 of the 17 known sex contacts by POR sequencing and from 15 of the 17 by OPA typing. Compared to OPA typing, which relies on interpretation of bands in a gel, DNA sequence data offer the advantage of being objective and portable. As costs for sequencing decline, the method should become affordable for most laboratory personnel who wish to type gonococcal strains.

scholarly journals Mapping Microbiome Signatures Associated With Antibiotic Usage On A Swine Production Farm Using Amplicon And Shotgun Data

2021 ◽  
Author(s):  
Adrian Muwonge ◽  
Jolinda Pollock ◽  
Shih Barbara ◽  
Michael R. Hutchings ◽  
Mark Bronsvoort ◽  
...  
Keyword(s):  
Sequence Data ◽  
Antibiotic Use ◽  
Efflux Pumps ◽  
Treated Group ◽  
Antibiotic Usage ◽  
Growing Pigs ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Swine Production ◽  
Shotgun Sequence

Abstract Background: High antimicrobial usage in swine production has the potential to create reservoirs of antimicrobial resistance (AMR) genes which are transferable to human pathogens via mobile genetic elements. Understanding microbial community responses to antibiotic use is central to unravelling transfer of such resistance genes. Our previous investigation revealed a scenario of optimal antibiotic activity associated with saturation of AMR genes on this farm. Here, we use amplicon and shotgun sequence data to investigate the microbiome signatures that underwrite such a phenomenon.Results: We generated 1.24 and 576 million high quality 16S rRNA gene amplicon and shotgun sequences from 24 porcine faecal samples, respectively. The ratio of taxa detection at genus level between the two methods was 1:24. Using shotgun sequence data, 235 unique AMR genes, 122 modes of action and 17 antibiotic classes were identified using the MEGARes AMR database. Antibiotic usage in growing pigs was significantly associated with microbial and AMR resistome structural and compositional changes detectable two weeks after antibiotic initiation. These were characterised by a down regulation of MDR efflux pumps and an up regulation of macrolide-specific efflux pumps in the growing pigs (treated-group) linked to lower abundance of Verrucomicrobiaeceae. In the sows (non-treated group), a potentially undetected infection, was characterised by a high abundance of pathogenic viral sequences, microbial structural changes i.e. family Alcaligenaceae, and an up regulation of beta-lactamases, including MDR efflux pumps. We assembled 682 near complete bacterial genomes revealing that a large proportion of the resistome is carried by Firmicutes and Proteobacteria, specifically multi-class gene carriage by Clostridium species and Escherichia coli, which occurred exclusively in the treatment group.Conclusion: Microbiome signatures i.e. microbial structure, composition and resistome carriage associated with antibiotic-use can be cost effectively screened with amplicon sequencing but their granularity unravelled using shotgun metagenomic data.

scholarly journals Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

2007 ◽  
Vol 3 (9) ◽  
pp. e181 ◽  
Author(s):  
Can Alkan ◽  
Mario Ventura ◽  
Nicoletta Archidiacono ◽  
Mariano Rocchi ◽  
S. Cenk Sahinalp ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Centromeric Dna ◽  
Shotgun Sequence ◽  
Whole Genome Shotgun Sequence ◽  
Genome Shotgun Sequence

scholarly journals Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Anton Lavrinienko ◽  
Eugene Tukalenko ◽  
Timothy A. Mousseau ◽  
Luke R. Thompson ◽  
Rob Knight ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Community Composition ◽  
Small Mammal ◽  
Bank Vole ◽  
Sequence Data ◽  
Myodes Glareolus ◽  
Wild Rodents ◽  
Bacterial Genomes ◽  
Shotgun Sequence ◽  
Essential Services

Abstract Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents.

scholarly journals The Identification of Pats1, a Novel Gene Locus Required for Cytokinesis in Dictyostelium discoideum

2003 ◽  
Vol 14 (1) ◽  
pp. 14-25 ◽  
Author(s):  
Jonathan C. Abysalh ◽  
Lisa L. Kuchnicki ◽  
Denis A. Larochelle
Keyword(s):  
Cell Line ◽  
Dictyostelium Discoideum ◽  
Restriction Enzyme ◽  
Gene Locus ◽  
Sequence Data ◽  
Mutant Cell ◽  
Genomic Region ◽  
Phenotypic Characterization ◽  
Regulatory Domains

Here, we describe the identification and characterization of the cytokinesis-deficient mutant cell line 17HG5, which was generated in a restriction enzyme–mediated integration mutagenesis screen designed to isolate genes required for cytokinesis in Dictyostelium discoideum. Phenotypic characterization of the 17HG5 cell line revealed no apparent defects in the global functionality of the actomyosin cytoskeleton except for the observed cytokinesis defect when grown in suspension culture. Plasmid rescue was used to identify the disrupted gene locus (pats1; protein associated with the transduction of signal 1) that caused the cytokinesis defect. Disruption of the pats1 locus was recreated through homologous recombination in several independent cell lines, each recapitulating the cytokinesis-defective phenotype and thereby confirming that this gene locus is important for proper cytokinesis. Sequence data obtained by analysis of the genomic region flanking the inserted restriction enzyme–mediated integration plasmid revealed an 8892-bp genomic open reading frame encoding a 2964-amino-acid protein. The putative pats1 protein contains 3 regulatory domains (RI-phosphatase, RII-GTP–binding, R-III protein kinase), 13 leucine-rich repeats, and 8 WD-40 repeats. These regulatory domains coupled with the protein–protein interacting domains suggest that pats1 is involved in signal transduction during cytokinesis inDictyostelium.

scholarly journals Finished bacterial genomes from shotgun sequence data

2012 ◽  
Vol 22 (11) ◽  
pp. 2270-2277 ◽  
Author(s):  
F. J. Ribeiro ◽  
D. Przybylski ◽  
S. Yin ◽  
T. Sharpe ◽  
S. Gnerre ◽  
...  
Keyword(s):  
Sequence Data ◽  
Bacterial Genomes ◽  
Shotgun Sequence
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