Dynamic of Mutational Events in Variable Number Tandem Repeats ofEscherichia coliO157:H7

VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenicE. coliO157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05to 1.8 × 10−03mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

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Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples

Genetics Research International ◽

10.1155/2018/8090469 ◽

2018 ◽

Vol 2018 ◽

pp. 1-5

Author(s):

Fidelis Charles Bugoye ◽

Elias Mulima ◽

Gerald Misinzo

Keyword(s):

Y Chromosome ◽

Mutation Rate ◽

Standard Error ◽

Tandem Repeats ◽

Dna Typing ◽

Paternity Testing ◽

Mutation Rates ◽

Buccal Swab ◽

Age Difference ◽

Rate Analysis

Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10−3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10−3 (6.41x10−4 - 6.013x10−3) at 95% CI. Furthermore the mean fathers’ age with at least one mutation at son’s birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son’s birth was 26.781 years with standard error of 0.609. The results shows that fathers’ age at son’s birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.

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Unusual mtDNA Control Region Length Heteroplasmy in the COS-7 Cell Line

Genes ◽

10.3390/genes11060607 ◽

2020 ◽

Vol 11 (6) ◽

pp. 607

Author(s):

Nataliya Kozhukhar ◽

Sunil Mitta ◽

Mikhail F. Alexeyev

Keyword(s):

Mitochondrial Genome ◽

Cell Line ◽

Control Region ◽

Tandem Repeats ◽

Variable Number ◽

Length Heteroplasmy ◽

Repeat Units ◽

Chlorocebus Aethiops ◽

Region Length ◽

Transcription And Replication

The COS-7 cell line is a workhorse of virology research. To expand this cell line’s utility and to enable studies on mitochondrial DNA (mtDNA) transcription and replication, we determined the complete nucleotide sequence of its mitochondrial genome by Sanger sequencing. In contrast to other available mtDNA sequences from Chlorocebus aethiops, the mtDNA of the COS-7 cell line was found to contain a variable number of perfect copies of a 108 bp unit tandemly repeated in the control region. We established that COS-7 cells are heteroplasmic with at least two variants being present: with four and five repeat units. The analysis of the mitochondrial genome sequences from other primates revealed that tandem repeats are absent from examined mtDNA control regions of humans and great apes, but appear in lower primates, where they are present in a homoplasmic state. To our knowledge, this is the first report of mtDNA length heteroplasmy in primates.

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Effect of Repeat Copy Number on Variable-Number Tandem Repeat Mutations in Escherichia coli O157:H7

Journal of Bacteriology ◽

10.1128/jb.00001-06 ◽

2006 ◽

Vol 188 (12) ◽

pp. 4253-4263 ◽

Cited By ~ 75

Author(s):

Amy J. Vogler ◽

Christine Keys ◽

Yoshimi Nemoto ◽

Rebecca E. Colman ◽

Zack Jay ◽

...

Keyword(s):

Escherichia Coli ◽

Mismatch Repair ◽

Mutation Rate ◽

Tandem Repeat ◽

Copy Number ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Mutation Rates ◽

Repeat Copy Number ◽

Repeat Copy

ABSTRACT Variable-number tandem repeat (VNTR) loci have shown a remarkable ability to discriminate among isolates of the recently emerged clonal pathogen Escherichia coli O157:H7, making them a very useful molecular epidemiological tool. However, little is known about the rates at which these sequences mutate, the factors that affect mutation rates, or the mechanisms by which mutations occur at these loci. Here, we measure mutation rates for 28 VNTR loci and investigate the effects of repeat copy number and mismatch repair on mutation rate using in vitro-generated populations for 10 E. coli O157:H7 strains. We find single-locus rates as high as 7.0 × 10−4 mutations/generation and a combined 28-locus rate of 6.4 × 10−4 mutations/generation. We observed single- and multirepeat mutations that were consistent with a slipped-strand mispairing mutation model, as well as a smaller number of large repeat copy number mutations that were consistent with recombination-mediated events. Repeat copy number within an array was strongly correlated with mutation rate both at the most mutable locus, O157-10 (r 2 = 0.565, P = 0.0196), and across all mutating loci. The combined locus model was significant whether locus O157-10 was included (r 2 = 0.833, P < 0.0001) or excluded (r 2 = 0.452, P < 0.0001) from the analysis. Deficient mismatch repair did not affect mutation rate at any of the 28 VNTRs with repeat unit sizes of >5 bp, although a poly(G) homomeric tract was destabilized in the mutS strain. Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat mutations, and their relative frequencies based upon our empirical mutation rate data.

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Development of a new nomenclature for Salmonella Typhimurium multilocus variable number of tandem repeats analysis (MLVA)

Eurosurveillance ◽

10.2807/ese.14.15.19174-en ◽

2009 ◽

Vol 14 (15) ◽

Author(s):

J T Larsson ◽

M Torpdahl ◽

R F Petersen ◽

G Sørensen ◽

B A Lindstedt ◽

...

Keyword(s):

Salmonella Typhimurium ◽

Tandem Repeats ◽

Fragment Size ◽

Foodborne Pathogen ◽

Variable Number ◽

Size Analysis ◽

Fragment Analysis ◽

Repeat Units ◽

Reference Strains ◽

Selection Of

Multilocus variable number of tandem repeats analysis (MLVA) has recently become a widely used highly discriminatory molecular method for typing of the foodborne pathogen Salmonella Typhimurium. This method is based on amplification and fragment size analysis of five repeat loci. To be able to easily compare MLVA results between laboratories there is a need for a simple and definitive nomenclature for MLVA profiles. Based on MLVA results for all human S. Typhimurium isolates in Denmark from the last five years and sequence analysis of a selection of these isolates, we propose a MLVA nomenclature that indicates the actual number of repeat units in each locus. This nomenclature is independent of the equipment used for fragment analysis and, in principle, independent of the primers used. A set of reference strains is developed that can be used for easy normalisation of fragment sizes in each laboratory.

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Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes

Genes ◽

10.3390/genes10070542 ◽

2019 ◽

Vol 10 (7) ◽

pp. 542

Author(s):

Kim ◽

Song ◽

Ha ◽

Moon ◽

Kim ◽

...

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Tandem Repeats ◽

Lentinula Edodes ◽

Mechanistic Model ◽

Variable Number ◽

Type I ◽

Complementary Sequence ◽

Repeat Units ◽

Variable Number Tandem Repeats

Variable number tandem repeats (VNTRs) in mitochondrial DNA (mtDNA) of Lentinula edodes are of interest for their role in mtDNA variation and their application as genetic marker. Sequence analysis of three L. edodes mtDNAs revealed the presence of VNTRs of two categories. Type I VNTRs consist of two types of repeat units in a symmetric distribution, whereas Type II VNTRs contain tandemly arrayed repeats of 7- or 17-bp DNA sequences. The number of repeat units was variable depending on the mtDNA of different strains. Using the variations in VNTRs as a mitochondrial marker and the A mating type as a nuclear type marker, we demonstrated that one of the two nuclei in the donor dikaryon preferentially enters into the monokaryotic cytoplasm to establish a new dikaryon which still retains the mitochondria of the monokaryon in the individual mating. Interestingly, we found 6 VNTRs with newly added repeat units from the 22 mates, indicating that elongation of VNTRs occurs during replication of mtDNA. This, together with comparative analysis of the repeating pattern, enables us to propose a mechanistic model that explains the elongation of Type I VNTRs through reciprocal incorporation of basic repeat units, 5’-TCCCTTTAGGG-3’ and its complementary sequence (5’-CCCTAAAGGGA-3’).

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Population-Scale Sequencing Data Enables Precise Estimates of Y-STR Mutation Rates

10.1101/036590 ◽

2016 ◽

Cited By ~ 2

Author(s):

Thomas Willems ◽

Melissa Gymrek ◽

G. David Poznik ◽

Chris Tyler-Smith ◽

Yaniv Erlich ◽

...

Keyword(s):

Tandem Repeats ◽

De Novo ◽

Mutation Rates ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Repeat Units ◽

Y Chromosomes ◽

Potential Applications ◽

Population Scale ◽

Using Data

AbstractShort Tandem Repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs using capillary electrophoresis and pedigree-based designs. While this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y-chromosome STRs (Y-STRs) with 2-6 base pair repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y-chromosomes of father-son pairs, and imputed Y-STR genotypes.

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