Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery

AbstractAlthough it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multi-locus sequencing typing, have not been quantified. By developing and analyzing 720 Listeria monocytogenes, Salmonella enterica, and Escherichia coli short-read datasets, we demonstrate that within-species contamination causes errors that confound clustering analyses, while between-species contamination generally does not. Contaminant reads mapping to references or becoming incorporated into chimeric sequences during assembly are the sources of those errors. Contamination sufficient to influence clustering analyses is present in public sequence databases.

Download Full-text

Single nucleotide polymorphism in the rpoB gene Mycobacterium tuberculosis from Papua-Indonesia and its impact on rifampicin resistance: A whole genome sequencing analysis

Microbiology Indonesia ◽

10.5454/mi.15.2.1 ◽

2021 ◽

Vol 15 (2) ◽

pp. 1

Author(s):

Yustinus Maladan ◽

Tri Wahyuni ◽

Hana Krismawati

Keyword(s):

Single Nucleotide Polymorphism ◽

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Rna Polymerase ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide

In the antibiotic era, Tuberculosis (TB) drugs resistance especially Rifampicin (RIF) is highly reported around the world. Resistance of RIF is caused by the mutation of genes that associated with RIF receptor. The aims of this study are detecting the Single Nucleotide Polymorphism of Rifampicin resistant genes using Whole Genome Sequencing (WGS) and analysing the profile of protein changing caused by SNP. Twenty Mycobacterium tuberculosis culture samples were passed on WGS procedure and 19 samples were adequate to further bioinformatics analysis. Single Nucleotide Polymorphisms Analysis was done using TBprofiler. Based on TBProfiler, seventeen samples were resistant to rifampicin. The mutations that cause the resistance are S450L, D435Y, H445Y, 430P, Q432K. Other Single Nucleotide Polymorphisms H835R, V534M and R224C were also found. The H835R mutants are present together with the S450L, V534M with S450L mutants, and R224C with Q432K mutants. Native protein for RNA Polymerase Subunit β used was the result of separation from the crystal structure of Mycobacterium tuberculosis H37Rv RNA polymerase (PDB: 5UHB). Binding affinity RIF to RNA Polymerase Subunit β calculated using AutoDock vina. Construction of mutant 3D structures using FoldX5. From the analysis, it was found that seventeen samples were resistant to rifampicin and two samples did not contain SNP which could cause resistance to rifampicin.

Download Full-text

Accurate Phylogenetic Relationships Among Mycobacterium bovis Strains Circulating in France Based on Whole Genome Sequencing and Single Nucleotide Polymorphism Analysis

Frontiers in Microbiology ◽

10.3389/fmicb.2019.00955 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 7

Author(s):

Amandine Hauer ◽

Lorraine Michelet ◽

Thierry Cochard ◽

Maxime Branger ◽

Javier Nunez ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mycobacterium Bovis ◽

Phylogenetic Relationships ◽

Polymorphism Analysis ◽

Whole Genome ◽

Single Nucleotide Polymorphism Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide

Download Full-text

Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue

Journal of Assisted Reproduction and Genetics ◽

10.1007/s10815-019-01588-6 ◽

2019 ◽

Vol 36 (12) ◽

pp. 2525-2531

Author(s):

Qian Geng ◽

Xiaoli Cui ◽

Yaqi Zhang ◽

Lijuan Zhang ◽

Cai Zhang ◽

...

Keyword(s):

Mass Spectrometry ◽

Single Nucleotide Polymorphism ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uniparental Disomy ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Quadratic Curve ◽

Low Coverage

Abstract Purpose To establish a single-nucleotide polymorphism-based analysis (SBA) method to identify triploidy in the miscarriage tissue by using low-coverage whole-genome sequencing (LC-WGS). Methods The method was established by fitting a quadratic curve model by counting the distribution of three heterozygous mutation content intervals. The triploid test result was mainly determined by the opening direction and the axis of symmetry of the quadratic curve, and Z test between the same batch samples was also used for auxiliary judgment. Results Two hundred thirteen diploid samples and 8 triploid samples were used for establishment of the analytical method and 203 unknown samples were used for blind testing. In the blind testing, we found 2 cases positive for triploidy. After chromosome microarray analysis (CMA) and mass spectrometry verification, we found that both samples were true positives. We randomly selected 5 samples from the negative samples for mass spectrometry verification, and the results showed that these samples were all true negatives. Conclusions Our method achieved accurate detection of triploidy in the miscarriage tissue and has the potential to detect more chromosomal abnormality types such as uniparental disomy (UPD) using a single LC-WGS approach.

Download Full-text

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

Journal of Clinical Microbiology ◽

10.1128/jcm.01280-15 ◽

2015 ◽

Vol 53 (10) ◽

pp. 3334-3340 ◽

Cited By ~ 77

Author(s):

Angela J. Taylor ◽

Victoria Lappi ◽

William J. Wolfgang ◽

Pascal Lapierre ◽

Michael J. Palumbo ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Outbreak Detection ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Molecular Subtyping ◽

Foodborne Outbreaks

Salmonella entericaserovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis ofS. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmentalS. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of theS. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method forS. Enteritidis.

Download Full-text