Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes

Nature ◽  
2008 ◽  
Vol 455 (7209) ◽  
pp. 105-108 ◽  
Author(s):  
Dacheng Tian ◽  
Qiang Wang ◽  
Pengfei Zhang ◽  
Hitoshi Araki ◽  
Sihai Yang ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Nucleotide Mutation

scholarly journals A Novel Single-Nucleotide Mutation in a CLAVATA3 Gene Homolog Controls a Multilocular Silique Trait in Brassica rapa L.

2014 ◽  
Vol 7 (12) ◽  
pp. 1788-1792 ◽  
Author(s):  
Chuchuan Fan ◽  
Yudi Wu ◽  
Qingyong Yang ◽  
Yang Yang ◽  
Qingwei Meng ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Nucleotide Mutation

scholarly journals Loss of Heterozygosity and Base Mutation Rates Vary Among Saccharomyces cerevisiae Hybrid Strains

2020 ◽  
Vol 10 (9) ◽  
pp. 3309-3319 ◽  
Author(s):  
Ajith V Pankajam ◽  
Suman Dash ◽  
Asma Saifudeen ◽  
Abhishek Dutta ◽  
Koodali T Nishant
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Loss Of Heterozygosity ◽  
Mutation Rates ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Specific Variation ◽  
Chromosomal Changes ◽  
Species Specific

Abstract A growing body of evidence suggests that mutation rates exhibit intra-species specific variation. We estimated genome-wide loss of heterozygosity (LOH), gross chromosomal changes, and single nucleotide mutation rates to determine intra-species specific differences in hybrid and homozygous strains of Saccharomyces cerevisiae. The mutation accumulation lines of the S. cerevisiae hybrid backgrounds - S288c/YJM789 (S/Y) and S288c/RM11-1a (S/R) were analyzed along with the homozygous diploids RM11, S288c, and YJM145. LOH was extensive in both S/Y and S/R hybrid backgrounds. The S/Y background also showed longer LOH tracts, gross chromosomal changes, and aneuploidy. Short copy number aberrations were observed in the S/R background. LOH data from the S/Y and S/R hybrids were used to construct a LOH map for S288c to identify hotspots. Further, we observe up to a sixfold difference in single nucleotide mutation rates among the S. cerevisiae S/Y and S/R genetic backgrounds. Our results demonstrate LOH is common during mitotic divisions in S. cerevisiae hybrids and also highlight genome-wide differences in LOH patterns and rates of single nucleotide mutations between commonly used S. cerevisiae hybrid genetic backgrounds.

Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation

The Analyst ◽  
2019 ◽  
Vol 144 (7) ◽  
pp. 2284-2290 ◽  
Author(s):  
Wei Zhou ◽  
Ze Yu ◽  
Ge Ma ◽  
Tian Jin ◽  
Yunchao Li ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Thioflavin T ◽  
Duplex Dna ◽  
Single Nucleotide ◽  
Single Nucleotide Mutation ◽  
Double Stranded Dna ◽  
Nucleotide Mutation

Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).

scholarly journals De novo mutations across 1,465 diverse genomes reveal novel mutational insights and reductions in the Amish founder population

2019 ◽  
Author(s):  
Michael D. Kessler ◽  
Douglas P. Loesch ◽  
James A. Perry ◽  
Nancy L. Heard-Costa ◽  
Brian E. Cade ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mutation Rate ◽  
De Novo ◽  
Population Level ◽  
Mutation Rates ◽  
Founder Population ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Nucleotide Mutation ◽  
Rare Genetic Variation

Abstractde novo Mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) program, we directly estimate and analyze DNM counts, rates, and spectra from 1,465 trios across an array of diverse human populations. Using the resulting call set of 86,865 single nucleotide DNMs, we find a significant positive correlation between local recombination rate and local DNM rate, which together can explain up to 35.5% of the genome-wide variation in population level rare genetic variation from 41K unrelated TOPMed samples. While genome-wide heterozygosity does correlate weakly with DNM count, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, interestingly, we do find significantly fewer DNMs in Amish individuals compared with other Europeans, even after accounting for parental age and sequencing center. Specifically, we find significant reductions in the number of T→C mutations in the Amish, which seems to underpin their overall reduction in DNMs. Finally, we calculate near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by non-additive genetic effects and/or the environment, and that a less mutagenic environment may be responsible for the reduced DNM rate in the Amish.SignificanceHere we provide one of the largest and most diverse human de novo mutation (DNM) call sets to date, and use it to quantify the genome-wide relationship between local mutation rate and population-level rare genetic variation. While we demonstrate that the human single nucleotide mutation rate is similar across numerous human ancestries and populations, we also discover a reduced mutation rate in the Amish founder population, which shows that mutation rates can shift rapidly. Finally, we find that variation in mutation rates is not heritable, which suggests that the environment may influence mutation rates more significantly than previously realized.

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