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 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 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 A cornucopia of research resources for the fourth rodent malaria parasite species

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jane M. Carlton
Keyword(s):  
Malaria Parasite ◽  
Parasite Species ◽  
First Century ◽  
Model Systems ◽  
Rodent Malaria Parasite ◽  
Malaria Parasites ◽  
Rodent Malaria ◽  
Human Malaria ◽  
Plasmodium Vinckei ◽  
Research Resources

AbstractThe study of human malaria caused by species of Plasmodium has undoubtedly been enriched by the use of model systems, such as the rodent malaria parasites originally isolated from African thicket rats. A significant gap in the arsenal of resources of the species that make up the rodent malaria parasites has been the lack of any such tools for the fourth of the species, Plasmodium vinckei. This has recently been rectified by Abhinay Ramaprasad and colleagues, whose pivotal paper published in BMC Biology describes a cornucopia of new P. vinckei ‘omics datasets, mosquito transmission experiments, transfection protocols, and virulence phenotypes, to propel this species firmly into the twenty-first century.

scholarly journals Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fetulhak Abdurahman ◽  
Kinde Anlay Fante ◽  
Mohammed Aliy
Keyword(s):  
Object Detection ◽  
Malaria Parasite ◽  
Blood Smear ◽  
Clustering Algorithm ◽  
State Of The Art ◽  
Detection Accuracy ◽  
Small Object ◽  
Thick Blood Smear ◽  
Malaria Parasites ◽  
Microscopic Images

Abstract Background Manual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the “gold standard” for malaria diagnosis. One of the drawbacks of this method is that its accuracy, consistency, and diagnosis speed depend on microscopists’ diagnostic and technical skills. It is difficult to get highly skilled microscopists in remote areas of developing countries. To alleviate this problem, in this paper, we propose to investigate state-of-the-art one-stage and two-stage object detection algorithms for automated malaria parasite screening from microscopic image of thick blood slides. Results YOLOV3 and YOLOV4 models, which are state-of-the-art object detectors in accuracy and speed, are not optimized for detecting small objects such as malaria parasites in microscopic images. We modify these models by increasing feature scale and adding more detection layers to enhance their capability of detecting small objects without notably decreasing detection speed. We propose one modified YOLOV4 model, called YOLOV4-MOD and two modified models of YOLOV3, which are called YOLOV3-MOD1 and YOLOV3-MOD2. Besides, new anchor box sizes are generated using K-means clustering algorithm to exploit the potential of these models in small object detection. The performance of the modified YOLOV3 and YOLOV4 models were evaluated on a publicly available malaria dataset. These models have achieved state-of-the-art accuracy by exceeding performance of their original versions, Faster R-CNN, and SSD in terms of mean average precision (mAP), recall, precision, F1 score, and average IOU. YOLOV4-MOD has achieved the best detection accuracy among all the other models with a mAP of 96.32%. YOLOV3-MOD2 and YOLOV3-MOD1 have achieved mAP of 96.14% and 95.46%, respectively. Conclusions The experimental results of this study demonstrate that performance of modified YOLOV3 and YOLOV4 models are highly promising for detecting malaria parasites from images captured by a smartphone camera over the microscope eyepiece. The proposed system is suitable for deployment in low-resource setting areas.

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.

scholarly journals Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cui Zhang ◽  
Cihan Oguz ◽  
Sue Huse ◽  
Lu Xia ◽  
Jian Wu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Malaria Parasite ◽  
Vaccine Development ◽  
De Novo ◽  
Gene Families ◽  
Plasmodium Yoelii ◽  
Control Measures ◽  
Effective Control ◽  
Malaria Parasites ◽  
Rodent Malaria

Abstract Background Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. Results We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. Conclusions The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.

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
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