scholarly journals Development of Microsatellites: A Powerful Genetic Marker

2016 ◽  
Vol 13 (1) ◽  
pp. 152-172 ◽  
Author(s):  
M Moniruzzaman ◽  
R Khatun ◽  
Zahira Yaakob ◽  
M S Khan ◽  
A A Mintoo
Keyword(s):  
Tandem Repeats ◽  
Genomic Library ◽  
De Novo ◽  
Genome Mapping ◽  
Variable Number ◽  
Genomic Libraries ◽  
Microsatellite Isolation ◽  
Major Disadvantage ◽  
A Genome ◽  
Variable Number Tandem Repeats

The tandem repeats, conserved short segments of DNA, which are found in all prokaryotic and eukaryotic genomes, are called microsatellites. It is also known as variable number tandem repeats (VNTRs), simple sequence repeats (SSRs) and short tandem repeats (STRs). Microsatellites present in both coding and non-coding regions of a genome. The high polymorphism of microsatellites makes them powerful genetic markers for genome mapping of many organisms. It is also suitable for ancient and forensic DNA studies for population genetics and conservation of biological resources. The major disadvantage of microsatellites is that for the first time they need to be isolated de novo from most species being examined. The task of microsatellite isolation is quite cumbersome involving in terms of effort and time, because it traditionally involves screening of genomic libraries. Cross-species amplification, Mining microsatellites from nucleotide sequenced data and Genomic library- based method are general methods of microsatellite isolation.  Cross-species method may not effective for all species, Data mining is not applicable if there is no or limited data of DNA sequence. Genomic library based method is the best choice. Traditional protocol, primer extension protocol, selective hybridization, and Fast Isolation by AFLP of Sequences containing repeats (FIASCO) are the protocols of microsatellite development based on genomic library.  FIASCO is the best protocol ever developed.The Agriculturists 2015; 13(1) 152-172

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 Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

scholarly journals Combinatorial interaction between two human serotonin transporter gene variable number tandem repeats and their regulation by CTCF

2010 ◽  
Vol 112 (1) ◽  
pp. 296-306 ◽  
Author(s):  
Fahad R. Ali ◽  
Sylvia A. Vasiliou ◽  
Kate Haddley ◽  
Ursula M. Paredes ◽  
Julian C. Roberts ◽  
...  
Keyword(s):  
Serotonin Transporter ◽  
Tandem Repeats ◽  
Variable Number ◽  
Serotonin Transporter Gene ◽  
Transporter Gene ◽  
Variable Number Tandem Repeats

scholarly journals Correlation Between Auto-antibodies to Survivin and MUC1 Variable Number Tandem Repeats in Colorectal Cancer

2012 ◽  
Vol 13 (11) ◽  
pp. 5557-5562 ◽  
Author(s):  
Yu-Qian Wang ◽  
Hai-Hong Zhang ◽  
Chen-Lu Liu ◽  
Qiu Xia ◽  
Hui Wu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tandem Repeats ◽  
Variable Number ◽  
Variable Number Tandem Repeats

scholarly journals Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats

2021 ◽  
pp. gr.275560.121
Author(s):  
Meredith M Course ◽  
Arvis Sulovari ◽  
Kathryn Gudsnuk ◽  
Evan E Eichler ◽  
Paul N Valdmanis
Keyword(s):  
Tandem Repeats ◽  
Variable Number ◽  
Nucleotide Variation ◽  
Specific Variable ◽  
Variable Number Tandem Repeats ◽  
Human Specific

scholarly journals Polymorphism of Interleukin 1B May Modulate the Risk of Ischemic Stroke in Polish Patients

Medicina ◽  
2019 ◽  
Vol 55 (9) ◽  
pp. 558 ◽  
Author(s):  
Gorący ◽  
Kaczmarczyk ◽  
Ciechanowicz ◽  
Lewandowska ◽  
Jakubiszyn ◽  
...  
Keyword(s):  
Risk Factor ◽  
Ischemic Stroke ◽  
Tandem Repeats ◽  
Interleukin 1 ◽  
Variable Number ◽  
Control Group ◽  
Key Factors ◽  
Inflammatory Processes ◽  
Variable Number Tandem Repeats ◽  
The Relationship

Background and Objectives: Inflammation plays a crucial role in the pathophysiology of ischemic stroke (IS). Interleukin-1B and interleukin-1 receptor antagonists are key factors in inflammatory processes. Aims: The aims of our study were to evaluate the relationship between genetic variation in interleukin-1B (IL1B) rs1143627 and interleukin-1 receptor antagonist (IL1RN) variable-number-tandem-repeats (VNTR), and overall IS and subtype prevalence rates. Materials and Methods: The analysis included 147 hospitalized Polish patients with IS diagnosed using conventional criteria. The control group consisted of 119 healthy subjects. Genotypes were determined by polymerase chain reaction. Results: A significant association between rs1143627 and stroke was found. The -31C IL1B polymorphism showed an association with overall IS, OR = 2.30 (1.36–3.87) p = 0.020. An association was also detected for LVI (large vessel infarction) subtypes of stroke. After risk factor adjustment (age, diabetes mellitus, dyslipidemia), the C allele was found to be an independent risk factor for LVI, OR = 1.99 (1.05–3.79) p = 0.036. Significant association was not observed between IL1RN alleles and IS. Conclusions: Our results suggest that the C allele of IL1B rs1143627 may be associated with susceptibility to overall IS and LVI subtypes of stroke in the Polish population.

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