scholarly journals Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations

DNA Research ◽  
2019 ◽  
Vol 26 (3) ◽  
pp. 273-286 ◽  
Author(s):  
Roman Matyášek ◽  
Alena Kuderová ◽  
Eva Kutílková ◽  
Marek Kučera ◽  
Aleš Kovařík
Keyword(s):  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Structural Diversity ◽  
Structural Heterogeneity ◽  
Variable Number ◽  
Mutual Arrangement ◽  
Cucurbita Moschata ◽  
Sequence Motifs ◽  
Dna Conformations ◽  
High Selection

Abstract The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300–1250 bp) and R2 (290–643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.

Using the structural diversity of siderophore biosynthesis genes for intra-and interspecific differentiation of pathogenic yersinia

2021 ◽  
pp. 50-56
Author(s):  
Daria Aleksandrovna Kuznetsova ◽  
Aleksey Leonidovich Trukhachev ◽  
Violetta Aleksandrovna Rykova ◽  
Olga Nikolaevna Podladchikova
Keyword(s):  
Tandem Repeats ◽  
Variable Structure ◽  
Structural Diversity ◽  
Variable Number ◽  
Differential Diagnostics ◽  
Pcr Analysis ◽  
Unknown Variable ◽  
Siderophore Biosynthesis ◽  
Pathogenic Yersinia

The paper analyzes the siderophore biosynthesis genes that are located in the ysu and ynp loci of only Y. pestis and Y. pseudotuberculosis, have variable structure between different strains of both species and contain previously unknown variable number tandem repeats (VNTR). The purpose of the study was to assess the possibility of using these VNTR as genetic markers for intra-and interspecific differentiation of pathogenic Yersinia. Based on the novel VNTR-markers, three pairs of primers (ysu-interF/R, ilp1F/R и ilp2F/R) were designed and used for the in silico and in vitro PCR analysis of various Y.pestis and Y. pseudotuberculosis strains. All studied Y. pestis strains of the main subspecies (ssp pestis), unlike the strains of non-main subspecies and Y. pseudotuberculosis, did not give amplicon with ilp1F/R primers, since the area between them contains an IS100 element. To identify the strains of the main subspecies, the fourth pair of primers ilp1F-is100R was designed, allowing the most dangerous ssp pestis strains to be distinguished from the not dangerous non-main ssp strains. Y. pseudotuberculosis strains were characterized by a significant variety of amplicons with three pairs of primers, and which made it possible to carry out intraspecies strain genotyping. At the same time, for those strains whose serotype is known, the correlation between the serogroup and the genotype of the strains was observed. Analysis of the 1 serotype strains representing most sequenced Y. pseudotuberculosis strains allowed us to separate two gene groups differing from the rest of 1 serotype gene groups. The first one included the serotype 1a strains isolated from people in Europe, which are known to have the greatest pathogenetic potential. The other one was formed by serotype 1b strains isolated from people in Siberia and Primorye, which are characterized by the high epidemic potential. Thus, four pairs of primers designed in this study can be used to develop additional tests for the identification and differential diagnostics of the most dangerous Y. pestis ssp pestis and Y. pseudotuberculosis serotype 1a and 1b strains.

Characterization of the Gyrodactylus salaris Malmberg, 1957 (Platyhelminthes: Monogenea) ribosomal intergenic spacer (IGS) DNA

Parasitology ◽  
2000 ◽  
Vol 121 (5) ◽  
pp. 555-563 ◽  
Author(s):  
C. M. COLLINS ◽  
C. O. CUNNINGHAM
Keyword(s):  
Ribosomal Rna ◽  
Tandem Repeats ◽  
Gene Array ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Sequence Motifs ◽  
Ribosomal Rna Gene ◽  
Intergenic Spacers ◽  
Transcription Start Sites ◽  
Pcr Products

The intergenic spacer of the ribosomal RNA gene array from the monogenean Gyrodactylus salaris was isolated using PCR amplification. PCR products were cloned and sequenced. Three different fragments of 0·63, 1·0 and 2·62 kb, were consistently obtained. These showed homology at the 5′ and 3′ termini but differed in their overall size and intervening sequence. The 5′ end showed homology to various 28S ribosomal RNA gene sequences, suggesting that this represented the 3′ terminus of the G. salaris 28S ribosomal RNA gene. A number of features common to other eukaryotic intergenic spacers were found in the longest sequence, including A + T rich sequences, palindromic sequences and tandemly repeated elements. Two regions of 23 bp sequences arranged in non-identical tandem repeats were identified. There were 9 repeats in both regions, separated by 81 bp of non-repetitive sequence. The repeat units from the two regions shared some similarity at their 3′ ends. The G. salaris intergenic spacer sequence was examined for sequence motifs involved in the transcription of the ribosomal RNA genes in other species. Several regions with homology to transcription start sites were identified.

Quantitative evaluation of post-bone marrow transplant engraftment status using fluorescent-labeled variable number of tandem repeats

2000 ◽  
Vol 05 (2) ◽  
pp. 129-138
Author(s):  
Robert A. Luhm ◽  
Daniel B. Bellissimo ◽  
Arejas J. Uzgiris ◽  
William R. Drobyski ◽  
Martin J. Hessner
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Transplant ◽  
Quantitative Evaluation ◽  
Tandem Repeats ◽  
Marrow Transplant ◽  
Variable Number

Dopaminergic Genes Polymorphisms and Prefrontal Cortex Efficiency Among Obese People - Whether Gender is a Differentiating Factor?

2019 ◽  
Vol 19 (6) ◽  
pp. 405-418
Author(s):  
Maciej Bieliński ◽  
Natalia Lesiewska ◽  
Roman Junik ◽  
Anna Kamińska ◽  
Andrzej Tretyn ◽  
...  
Keyword(s):  
Prefrontal Cortex ◽  
Executive Functions ◽  
Tandem Repeats ◽  
Wisconsin Card Sorting Test ◽  
Variable Number ◽  
Card Sorting ◽  
Obese People ◽  
Perseverative Errors ◽  
Wisconsin Card Sorting ◽  
Sorting Test

Background:Obesity is a chronic condition associated with poorer cognitive functioning. Wisconsin Card Sorting Test (WCST) is a useful tool for evaluating executive functions. In this study, we assessed the association between dopaminergic gene polymorphisms: DAT1 (SLC6A3), COMTVal158Met, DRD4 (48-bp variable number of tandem repeats - VNTR) and WCST parameters to investigate the functions of the frontal lobes in obese individuals.Objective:To find the significant correlations between polymorphisms of DAT1, COMTVal158Met, DRD4 and executive functions in obese subjects.Methods:The analysis of the frequency of individual alleles was performed in 248 obese patients (179 women, 69 men). Evaluation of the prefrontal cortex function (operating memory and executive functions) was measured with the Wisconsin Card Sorting Test (WCST). Separate analyzes were performed in age subgroups to determine different activities and regulation of genes in younger and older participants.Results:Scores of WCST parameters were different in the subgroups of women and men and in the age subgroups. Regarding the COMT gene, patients with A/A and G/A polymorphisms showed significantly better WCST results in WCST_P, WCST_CC and WCST_1st. Regarding DAT1 men with L/L and L/S made less non-perseverative errors, which was statistically significant. In DRD4, significantly better WCST_1st results were found only in older women with S allele.Conclusion:Obtained results indicate the involvement of dopaminergic transmission in the regulation of prefrontal cortex function. Data analysis indicates that prefrontal cortex function may ensue, from different elements such as genetic factors, metabolic aspects of obesity, and hormonal activity (estrogen).

scholarly journals Molecular characteristics of Brucella melitensis isolates from humans in Qinghai Province, China

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhi-Jun Zhao ◽  
Ji-Quan Li ◽  
Li Ma ◽  
Hong-Mei Xue ◽  
Xu-Xin Yang ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Draft Genome ◽  
Geographic Origin ◽  
Variable Number ◽  
Human Brucellosis ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Qinghai Province ◽  
Variable Number Tandem Repeats

Abstract Background The prevalence of human brucellosis in Qinghai Province of China has been increasing rapidly, with confirmed cases distributed across 31 counties. However, the epidemiology of brucellosis transmission has not been fully elucidated. To characterize the infecting strains isolated from humans, multiple-locus variable-number tandem repeats analysis (MLVA) and whole-genome single-nucleotide polymorphism (SNP)-based approaches were employed. Methods Strains were isolated from two males blood cultures that were confirmed Brucella melitensis positive following biotyping and MLVA. Genomic DNA was extracted from these two strains, and whole-genome sequencing was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The two Brucella isolates were identified as B. melitensis biovar 3 (QH2019001 and QH2019005) following conventional biotyping and were found to have differences in their variable number tandem repeats (VNTRs) using MLVA-16. Phylogenetic examination assigned the 96 strains to five genotype groups, with QH2019001 and QH2019005 assigned to the same group, but different subgroups. Moreover, the QH2019005 strain was assigned to a new subgenotype, IIj, within genotype II. These findings were then combined to determine the geographic origin of the two Brucella strains. Conclusions Utilizing a whole-genome SNP-based approach enabled differences between the two B. melitensis strains to be more clearly resolved, and facilitated the elucidation of their different evolutionary histories. This approach also revealed that QH2019005 is a member of a new subgenotype (IIj) with an ancient origin in the eastern Mediterranean Sea.

scholarly journals Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tsung-Yu Lu ◽  
Katherine M. Munson ◽  
Alexandra P. Lewis ◽  
Qihui Zhu ◽  
Luke J. Tallon ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Traditional Approach ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Population Diversity ◽  
Protein Coding ◽  
Short Reads ◽  
Repeat Structure ◽  
Continental Population ◽  
Develop Software

AbstractVariable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

VNTR (variable number of tandem repeats) markers show loss of chromosome 17p sequences in human colorectal carcinomas

1988 ◽  
Vol 48 (3) ◽  
pp. 167-169 ◽  
Author(s):  
R.A. Lothe ◽  
Y. Nakamura ◽  
S. Woodward ◽  
T.G. Gedde-Dahl, Jr ◽  
R. White
Keyword(s):  
Tandem Repeats ◽  
Variable Number ◽  
Colorectal Carcinomas

scholarly journals Community-based geographical distribution of Mycobacterium ulcerans VNTR-genotypes from the environment and humans in the Nyong valley, Cameroon

2021 ◽  
Vol 49 (1) ◽  
Author(s):  
Francis Zeukeng ◽  
Anthony Ablordey ◽  
Solange E. Kakou-Ngazoa ◽  
Stephen Mbigha Ghogomu ◽  
David N’golo Coulibaly ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Tandem Repeats ◽  
Buruli Ulcer ◽  
Variable Number ◽  
Mycobacterium Ulcerans ◽  
Community Based ◽  
Human Samples ◽  
Route Of Transmission ◽  
Mode Of Transmission ◽  
Animal Reservoirs

Abstract Background Genotyping is a powerful tool for investigating outbreaks of infectious diseases and it can provide useful information such as identifying the source and route of transmission, and circulating strains involved in the outbreak. Genotyping techniques based on variable number of tandem repeats (VNTR) are instrumental in detecting heterogeneity in Mycobacterium ulcerans (MU) and also for discriminating MU from other mycobacteria species. Here, we describe and map the distribution of MU genotypes in Buruli ulcer (BU) endemic communities of the Nyong valley in Cameroon. We also tested the hypothesis of whether the suspected animal reservoirs of BU that share the human microhabitat are shedding contaminated fecal matters and saliva into their surrounding environments. Methods Environmental samples from suspected MU-risk factors and lesion swabs from human patients were sampled in BU-endemic communities and tested for the presence of MU by qPCR targeting three independent sequences (IS2404, IS2606, KR-B). Positive samples to MU were further genotyped by VNTR with confirmation by sequencing of four loci (MIRU1, Locus 6, ST1, Locus 19). Results MU was detected in environmental samples including water bodies (23%), biofilms (14%), detritus (10%), and in human patients (73%). MU genotypes D, W, and C were found both in environmental and human samples. The micro geo-distribution of MU genotypes from communities showed that genotype D is found both in environmental and human samples, while genotypes W and C are specific to environmental samples and human lesions, respectively. No obvious focal grouping of MU genotypes was observed at the community scale. An additional survey in the human microhabitat suggests that domestic and wild animals do not shed MU in their saliva and feces in sampled communities. Conclusions VNTR typing uncovered different MU genotypes circulating in the endemic communities of the Akonolinga district. A MU environmental genotype was found in patients, yet the mechanism of contamination remains to be investigated; and recovering MU in culture from the environment remains key priority to enable a better understanding of the mode of transmission of BU. We also conclude that excretions from suspected animals are unlikely to be major sources of MU in the Nyong Valley in Cameroon.

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