scholarly journals The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1094 ◽  
Author(s):  
Natalia Mazur-Panasiuk ◽  
Marek Walczak ◽  
Małgorzata Juszkiewicz ◽  
Grzegorz Woźniakowski
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Wild Boar ◽  
Tandem Repeats ◽  
African Swine Fever ◽  
Whole Genome Sequence ◽  
Reference Sequence ◽  
Nucleotide Sequencing ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
First Case

The African swine fever epidemic occurred in Poland at the beginning of 2014 and, up to date, the disease has been spreading mainly in the eastern part of the country. Unexpectedly, in November 2019 an infected wild boar case was confirmed in Lubuskie voivodship in western Poland. During the following weeks, several dozen African swine fever virus (ASFV)-positive animals were notified in the neighboring area, causing severe concern regarding further spread of the disease to the mostly pig-dense region in Poland, namely, Wielkopolskie voivodship. Moreover, almost a year after, several infected wild boar cases were confirmed for the first time in Germany, just beyond the Polish border, sending out a shock wave through the global pig market. The whole genome sequence of ASFV, isolated from the first case of ASF in western Poland, and three selected viruses from other affected areas, revealed the tandem repeat and single nucleotide polymorphism (SNP) variations in reference to the Georgia 2007/1 strain. These data, supported by the conventional sequencing of selected genomic regions from a total of 154 virus samples isolated between 2017 and 2020 in Poland, shed a new light on pathogen epidemiology. The sequence variations within the O174L gene detected in this study showed that cases identified in western Poland might be originating from the so-called southern Warsaw cluster. Moreover, the viruses originating from the northern Warsaw cluster do not possess single nucleotide polymorphism (SNP) mutations within the K145R and MGF 505-5R genes, which are specific to all of the other Polish ASFV strains. These results led to a conclusion of their distinct origin. Supporting these results, the nucleotide sequencing of I73R/I329L intergenic region revealed its new, previously undescribed variant, called IGR IV, with an additional three tandem repeats of 10 nucleotides in comparison to the reference sequence of the Georgia 2007/1 strain.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

scholarly journals Congenital Analbuminemia in a Korean Male Diagnosed with Single Nucleotide Polymorphism in the ALB Gene: The First Case Reported in Korea

2019 ◽  
Vol 60 (7) ◽  
pp. 700 ◽  
Author(s):  
Youngji Kim ◽  
Ye Seul Yang ◽  
Sung Sup Park ◽  
Man Jin Kim ◽  
Cheol Min Shin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
First Case

scholarly journals Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Anna Janowicz ◽  
Fabrizio De Massis ◽  
Massimo Ancora ◽  
Cesare Cammà ◽  
Claudio Patavino ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Brucella Melitensis ◽  
Reference Sequence ◽  
Snp Analysis ◽  
Phylogenetic Distance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

scholarly journals Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Arthur W. Pightling ◽  
James B. Pettengill ◽  
Yu Wang ◽  
Hugh Rand ◽  
Errol Strain
Keyword(s):  
Escherichia Coli ◽  
Single Nucleotide Polymorphism ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Single Nucleotide Polymorphism Discovery ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Short Read ◽  
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.

scholarly journals Rapid Detection of Aneuploidy (Trisomy 21) by Allele Quantification Combined with Melting Curves Analysis of Single-Nucleotide Polymorphism Loci

2003 ◽  
Vol 49 (7) ◽  
pp. 1087-1094 ◽  
Author(s):  
Genevieve Pont-Kingdon ◽  
Elaine Lyon
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Trisomy 21 ◽  
Tandem Repeats ◽  
Melting Curve ◽  
Curve Analysis ◽  
Chromosome 21 ◽  
Melting Curve Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Melting Curves

Abstract Background: Molecular approaches for the detection of chromosomal abnormalities will allow the development of rapid, cost-effective screening strategies. We present here a molecular alternative for the detection of aneuploidies and, more specifically, trisomy 21. Methods: We used the quantitative value of melting curve analysis of heterozygous genetic loci to establish a relative allelic count. The two alleles of a given single-nucleotide polymorphism (SNP) were differentiated by thermodynamic stability with a fluorescently labeled hybridization probe and were quantified by relative areas of derivative melting curves detected after fluorescence resonance energy transfer. Heterozygous SNPs provided internal controls for the assay. Results: We selected six SNPs, heterozygous in at least 30% of a random population, to form a panel of informative loci in the majority of a random population. After normalization to a heterozygous control, samples segregated into three categories; nontrisomic samples had mean allele ratios of 0.96–1.09, whereas trisomic samples had mean ratios of 1.84–2.09 or 0.46–0.61, depending on which allele was duplicated. Within-run mean CVs of ratios were 6.5–27%, and between-assay mean CVs were 13–24%. Conclusions: The use of melting curve analysis of multiple SNPs is an alternative to the use of small tandem repeats for the detection of trisomies. Because of the high density of SNPs, the approach may be specifically useful for very fine mapping of the regions of chromosome 21 that are critical for Down syndrome; it is also applicable to aneuploidies other than trisomy 21 and to specimens that are not amenable to cytogenetic analysis.

A single nucleotide polymorphism in the sheep κ-casein coding region

2005 ◽  
Vol 72 (3) ◽  
pp. 317-321 ◽  
Author(s):  
Maria Feligini ◽  
Slavica Vlaco ◽  
Vlatka Cubric Curik ◽  
Pietro Parma ◽  
GianFranco Greppi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Region ◽  
Reference Sequence ◽  
Mature Protein ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Conventional Pcr ◽  
Homozygous State ◽  
Single Nucleotide ◽  
Forward Primer

Genetic polymorphisms in CSN3 gene in Pag (Croatia), Sarda (Italy) and Pramenka (Serbia) sheep breeds were investigated. A single nucleotide polymorphism (SNP) was localized by sequence analysis (sequence submitted to GenBank under accession AY237637) relying on an original primer pair. Primers for sequencing (κ-casF and κ-casR) were designed on the available CSN3 sequences to amplify the genomic region encoding the major part of the mature protein (exon 4). An SNP was detected at position 237 of the sheep κ-casein mRNA (reference sequence: GenBank X51822), where a thymine was substituted for a cytosine. The SNP was typed by conventional PCR and SYBR Green I-based real-time PCR. C and T alleles were discriminated using a dedicated set of primers that consisted of one common forward primer (SNP-TC) and two reverse primers (SNP-T and SNP-C), the latter two differing in the 3′ end base and in the presence of a 12 bp poly-G tail in SNP-C. The SNP was found in both the heterozygous and the homozygous state in Sarda and Pramenka breeds, and in the heterozygous state only in the Pag breed. The observed allelic frequencies of the SNP were 0·12 in Pag, 0·27 in Sarda and 0·45 in Pramenka.

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