scholarly journals Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment

2019 ◽  
Vol 11 (7) ◽  
pp. 1971-1985 ◽  
Author(s):  
Marina McDew-White ◽  
Xue Li ◽  
Standwell C Nkhoma ◽  
Shalini Nair ◽  
Ian Cheeseman ◽  
...  
Keyword(s):  
False Negative ◽  
Natural Populations ◽  
Point Mutations ◽  
Length Change ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Single Infection ◽  
Independent Sequence ◽  
Duplicate Sequence ◽  
Microsatellite Mutation

Abstract Malaria parasites have small extremely AT-rich genomes: microsatellite repeats (1–9 bp) comprise 11% of the genome and genetic variation in natural populations is dominated by repeat changes in microsatellites rather than point mutations. This experiment was designed to quantify microsatellite mutation patterns in Plasmodium falciparum. We established 31 parasite cultures derived from a single parasite cell and maintained these for 114–267 days with frequent reductions to a single cell, so parasites accumulated mutations during ∼13,207 cell divisions. We Illumina sequenced the genomes of both progenitor and end-point mutation accumulation (MA) parasite lines in duplicate to validate stringent calling parameters. Microsatellite calls were 99.89% (GATK), 99.99% (freeBayes), and 99.96% (HipSTR) concordant in duplicate sequence runs from independent sequence libraries, whereas introduction of microsatellite mutations into the reference genome revealed a low false negative calling rate (0.68%). We observed 98 microsatellite mutations. We highlight several conclusions: microsatellite mutation rates (3.12 × 10−7 to 2.16 × 10−8/cell division) are associated with both repeat number and repeat motif like other organisms studied. However, 41% of changes resulted from loss or gain of more than one repeat: this was particularly true for long repeat arrays. Unlike other eukaryotes, we found no insertions or deletions that were not associated with repeats or homology regions. Overall, microsatellite mutation rates are among the lowest recorded and comparable to those in another AT-rich protozoan (Dictyostelium). However, a single infection (>1011 parasites) will still contain over 2.16 × 103 to 3.12 × 104 independent mutations at any single microsatellite locus.

scholarly journals Mode and tempo of microsatellite length change in a malaria parasite mutation accumulation experiment

2019 ◽  
Author(s):  
Marina McDew-White ◽  
Xue Li ◽  
Standwell C. Nkhoma ◽  
Shalini Nair ◽  
Ian Cheeseman ◽  
...  
Keyword(s):  
Single Cell ◽  
Malaria Parasite ◽  
Mutation Accumulation ◽  
Repeat Motif ◽  
Mutation Rates ◽  
Repeat Number ◽  
Malaria Parasites ◽  
Independent Sequence ◽  
Parasite Cell ◽  
Microsatellite Mutation

AbstractMicrosatellite sequences are widely assumed to evolve neutrally, but also play an important role in bacterial pathogenesis, human disease and transcript abundance. The malaria parasite Plasmodium falciparum genome is extraordinarily AT-rich, containing 132,449 microsatellites-stretches of perfect 1-9 bp repeats between 10-1000bp, which comprise 10.74% of the 23 Mb genome. This project was designed to determine the mode and tempo of microsatellite mutations in malaria parasites. We maintained 31 parasite lines derived from a single 3D7 parasite cell for 114-267 days, with frequent bottlenecking to a single cell to minimize effective population size, allowing us to measure mutations accumulated over ~13,207 mitotic divisions. We Illumina sequenced the genomes of both progenitor and end-point mutation accumulation (MA) parasite lines in duplicate to validate stringent calling parameters. Calls were 99.89% (GATK), 99.99% (freeBayes) and 99.96% (HipSTR) concordant in duplicate sequence runs from independent sequence libraries. We observed 98 microsatellite mutations, giving rates of 2.11 × 10-7 - 1.46 × 10-8 /cell division that were strongly influenced by repeat motif and array length. Mutation rate was low relative to other organisms. However, despite this, in a single infection (1011 parasites) there will be 1.46 × 103 - 2.11 × 104 independent mutations at any single microsatellite locus. Given that many microsatellites are found in promotors, introns, within or close to coding sequences, we suggest that they may be important regulators of transcriptional and phenotypic variation in this pathogen.Author summaryMutation is central to evolution: in pathogens, the rate of mutation may determine how rapidly drug resistance evolves or how effectively pathogens can escape immune attack. Malaria parasites have small extremely AT-rich genomes, and genetic variation in natural populations is dominated by repeat number changes in short tandem repeats (microsatellites) rather than point mutations. We therefore focused on quantifying microsatellite mutation. We established 31 parasite cultures in the laboratory all derived from a single parasite cell. These were maintained for 114-267 days with frequent reductions to a single cell, so parasites accumulated mutations during ~13,207 cell divisions. We sequenced the parasite genomes at the end of the experiment to count the mutations. We highlight several conclusions: like other organisms studied, microsatellite mutation rates are associated with both repeat number and repeat motif. However, 41% of changes resulted from loss or gain of more than one repeat: this was particularly true for long repeat arrays. Unlike other eukaryotes, we found no insertions or deletions that were not associated with repeats or homology regions. Overall, we found that microsatellite mutation rates in malaria were amongst the lowest recorded and comparable to those in another AT-rich protozoan (the slime mold Dictyostelium).

scholarly journals Estimation of microsatellite mutation rates in Drosophila melanogaster

2000 ◽  
Vol 76 (3) ◽  
pp. 323-326 ◽  
Author(s):  
JOSÉ FERNANDO VÁZQUEZ ◽  
TRINIDAD PÉREZ ◽  
JESÚS ALBORNOZ ◽  
ANA DOMÍNGUEZ
Keyword(s):  
Drosophila Melanogaster ◽  
Mutation Rate ◽  
Mutation Accumulation ◽  
Trinucleotide Repeats ◽  
Dinucleotide Repeat ◽  
The Other ◽  
Mutation Rates ◽  
Full Agreement ◽  
Single Addition ◽  
Microsatellite Mutation

Microsatellite mutations were studied in a set of 175 mutation accumulation lines, all of them independently derived from a completely homozygous population of Drosophila melanogaster and maintained under strong inbreeding during 80 generations. We assayed 28 microsatellites and detected two mutations. One mutation consisted of a single addition of a dinucleotide repeat and the other was a deletion of five trinucleotide repeats. The average mutation rate was 5·1 × 10−6, in full agreement with previous estimates from two different sets of mutation accumulation lines.

scholarly journals Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

2019 ◽  
Author(s):  
Eddie K. H. Ho ◽  
Fenner Macrae ◽  
Leigh C. Latta ◽  
Maia J. Benner ◽  
Cheng Sun ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Tandem Repeats ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Evolutionary Forces ◽  
Repeat Content ◽  
Long Time ◽  
Order Of Magnitude ◽  
Time Periods ◽  
Microsatellite Mutation

AbstractMicrosatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and are often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species and have rarely been compared across genotypes and populations and intraspecific differences in overall microsatellite content have rarely been explored. To investigate the accumulation of microsatellite DNA over long-and short-time periods, we quantified the abundance and genome-wide mutation rates in whole-genome sequences of 47 mutation accumulation (MA) lines and 12 non-MA lines derived from six different genotypes of the crustacean Daphnia magna collected from three populations (Finland, Germany, and Israel). Each genotype possessed a distinctive microsatellite profile and clustered according to their population of origin. During the period of mutation accumulation, we observed very high microsatellite mutation rates (a net change of −0.19 to 0.33 per copy per generation), which surpass rates reported from a closely-related congener, D. pulex, by an order of magnitude. Rates vary between microsatellite motifs and among genotypes, with those starting with high microsatellite content exhibiting greater losses and those with low microsatellite content exhibiting greater gains. Our results show that microsatellite mutation rates depend both on characteristics of the microsatellites and the genomic background. These context-dependent mutation dynamics may, in conjunction with other evolutionary forces that may differ among populations, explain the differential accumulation of repeat content in the genome over long time periods.

scholarly journals On the Rate and Linearity of Viability Declines in Drosophila Mutation-Accumulation Experiments: Genomic Mutation Rates and Synergistic Epistasis Revisited

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 797-806 ◽  
Author(s):  
James D Fry
Keyword(s):  
Mutation Rate ◽  
Average Rate ◽  
Natural Populations ◽  
Mutation Accumulation ◽  
High Rate ◽  
Deleterious Mutations ◽  
Order Of Magnitude ◽  
Contamination Event ◽  
Genomic Mutation ◽  
The 1960S

Abstract High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others’ effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi’s experiment as well as in Mukai’s, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai’s estimate of the genomic mutation rate is supported, that from Ohnishi’s experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai’s experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.

scholarly journals Nature of Deleterious Mutation Load in Drosophila

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1993-1999 ◽  
Author(s):  
Peter D Keightley
Keyword(s):  
Deleterious Mutation ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Mutation Load ◽  
Spontaneous Mutation Rate ◽  
A Minor ◽  
Chromosome I ◽  
Balancer Chromosomes ◽  
Balancer Chromosome

Much population genetics and evolution theory depends on knowledge of genomic mutation rates and distributions of mutation effects for fitness, but most information comes from a few mutation accumulation experiments in Drosophila in which replicated chromosomes are sheltered from natural selection by a balancer chromosome. I show here that data from these experiments imply the existence of a large class of minor viability mutations with approximately equivalent effects. However, analysis of the distribution of viabilities of chromosomes exposed to EMS mutagenesis reveals a qualitatively different distribution of effects lacking such a minor effects class. A possible explanation for this difference is that transposable element insertions, a common class of spontaneous mutation event in Drosophila, frequently generate minor viability effects. This explanation would imply that current estimates of deleterious mutation rates are not generally applicable in evolutionary models, as transposition rates vary widely. Alternatively, much of the apparent decline in viability under spontaneous mutation accumulation could have been nonmutational, perhaps due to selective improvement of balancer chromosomes. This explanation accords well with the data and implies a spontaneous mutation rate for viability two orders of magnitude lower than previously assumed, with most mutation load attributable to major effects.

Y-chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci

2004 ◽  
Vol 23 (2) ◽  
pp. 117-124 ◽  
Author(s):  
B. Myhre Dupuy ◽  
M. Stenersen ◽  
T. Egeland ◽  
B. Olaisen
Keyword(s):  
Mutation Rate ◽  
Mutation Rates ◽  
Microsatellite Mutation

scholarly journals Quantifying Microsatellite Mutation Rates from Intestinal Stem Cell Dynamics in Msh2-Deficient Murine Epithelium

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 655-665 ◽  
Author(s):  
Joseph Christopher ◽  
Ann-Sofie Thorsen ◽  
Sam Abujudeh ◽  
Filipe C. Lourenço ◽  
Richard Kemp ◽  
...  
Keyword(s):  
Stem Cell ◽  
Fold Increase ◽  
Mutation Rates ◽  
Wild Type ◽  
Cell Dynamics ◽  
Tissue Samples ◽  
Age Related ◽  
Increased Risk ◽  
Microsatellite Mutation ◽  
Risk Of Cancer

Microsatellite sequences have an enhanced susceptibility to mutation, and can act as sentinels indicating elevated mutation rates and increased risk of cancer. The probability of mutant fixation within the intestinal epithelium is dictated by a combination of stem cell dynamics and mutation rate. Here, we exploit this relationship to infer microsatellite mutation rates. First a sensitive, multiplexed, and quantitative method for detecting somatic changes in microsatellite length was developed that allowed the parallel detection of mutant [CA]n sequences from hundreds of low-input tissue samples at up to 14 loci. The method was applied to colonic crypts in Mus musculus, and enabled detection of mutant subclones down to 20% of the cellularity of the crypt (∼50 of 250 cells). By quantifying age-related increases in clone frequencies for multiple loci, microsatellite mutation rates in wild-type and Msh2-deficient epithelium were established. An average 388-fold increase in mutation per mitosis rate was observed in Msh2-deficient epithelium (2.4 × 10−2) compared to wild-type epithelium (6.2 × 10−5).

scholarly journals First Estimation of the Spontaneous Mutation Rate in Diatoms

2019 ◽  
Vol 11 (7) ◽  
pp. 1829-1837 ◽  
Author(s):  
Marc Krasovec ◽  
Sophie Sanchez-Brosseau ◽  
Gwenael Piganeau
Keyword(s):  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Model Organisms ◽  
Base Substitution ◽  
Unicellular Eukaryote ◽  
Fundamental Parameter ◽  
Secondary Endosymbiosis ◽  
Spontaneous Mutation Rate

Abstract Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.

Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci

Genetica ◽  
2008 ◽  
Vol 136 (3) ◽  
pp. 501-504 ◽  
Author(s):  
Zafer Bulut ◽  
Cory R. McCormick ◽  
David Gopurenko ◽  
Rod N. Williams ◽  
David H. Bos ◽  
...  
Keyword(s):  
Mutation Rates ◽  
Ambystoma Tigrinum ◽  
Tiger Salamander ◽  
Microsatellite Mutation ◽  
Ambystoma Tigrinum Tigrinum

scholarly journals Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1164
Author(s):  
Shona C. Moore ◽  
Rebekah Penrice-Randal ◽  
Muhannad Alruwaili ◽  
Nadine Randle ◽  
Stuart Armstrong ◽  
...  
Keyword(s):  
Viral Genome ◽  
False Negative ◽  
Point Mutations ◽  
Read Length ◽  
Diagnostic Tools ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Pathogenic Potential ◽  
Number Of Patients ◽  
Interferon Antagonism

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.

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