Abundant variation in microsatellites of the parasitic nematode Trichostrongylus tenuis and linkage to a tandem repeat

Johnson, Paul C. D.; Webster, Lucy M.I.; Adam, Aileen; Buckland, Robert; Dawson, Deborah A.; Keller, Lukas F.

doi:10.1016/j.molbiopara.2006.04.011

Cited by 46 publications

(41 citation statements)

References 61 publications

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“…The approximation s a accounts for 98.1% of the variation in s at n H ¼ 50 and .99.5% at n H $ 100. Although all microsatellite allele-frequency distributions will deviate from broken-stick expected frequencies to some extent, comparison of s calculated from data with s a simulated at the same H e and n H for data from 54 microsatellite loci (H e range, 0.27-0.90; n H range, 172-545) from aphids ( Johnson et al 2000), nematodes ( Johnson et al 2006), red foxes, and Ethiopian wolves (data kindly provided by P. Wandeler and D. A. Randall) suggests that the broken-stick model fits well to reality. The means of the simulated and real standard deviations were not significantly different (mean s a ¼ 0.0124, mean data s ¼ 0.0130, P ¼ 0.24, paired t-test), and the slope of the linear regression line (s ¼ 1.10s a À 0.0007, R 2 ¼ 0.62) did not differ significantly from 1 (t 52 ¼ 0.87, P ¼ 0.39).…”

Section: Discussionmentioning

confidence: 99%

Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data

2007

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The importance of quantifying and accounting for stochastic genotyping errors when analyzing microsatellite data is increasingly being recognized. This awareness is motivating the development of data analysis methods that not only take errors into consideration but also recognize the difference between two distinct classes of error, allelic dropout and false alleles. Currently methods to estimate rates of allelic dropout and false alleles depend upon the availability of error-free reference genotypes or reliable pedigree data, which are often not available. We have developed a maximum-likelihood-based method for estimating these error rates from a single replication of a sample of genotypes. Simulations show it to be both accurate and robust to modest violations of its underlying assumptions. We have applied the method to estimating error rates in two microsatellite data sets. It is implemented in a computer program, Pedant, which estimates allelic dropout and false allele error rates with 95% confidence regions from microsatellite genotype data and performs power analysis. Pedant is freely available at http:/ /www.stats.gla.ac. uk/$paulj/pedant.html.

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Section: Discussionmentioning

confidence: 99%

Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data

2007

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“…These findings are reflected in the relatively high frequency of SSR transferability among legume species (Pandian et al, 2000;Gutierrez et al, 2005). The contradictory view that microsatellites are derived from repetitive (high copy number) sequences is supported by several reports in plants (Ramsay et al, 1999;Temnykh et al, 2001;Koike et al, 2006;Tero et al, 2006), insects (Wilder and Hollocher, 2001;Meglecz et al, 2007;Van't Hof et al, 2007) and nematodes (Johnson et al, 2006), suggesting a link between transposable elements and microsatellite sequence. One theory is that the transposable element harboring the proto-microsatellite sequence distributes it genome-wide by transposition and this sequence subsequently develops into a full microsatellite.…”

Section: Introductionmentioning

confidence: 93%

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

Smýkal

Kalendar²,

Ford

et al. 2009

Heredity

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“…Microsatellites have been described in parasitology and used in some parasites of both humans and animals (9). Microsatellites are abundant in eukaryotic genomes and can mutate rapidly by loss or gain of repeat units (81,85). The wide variety of applications of microsatellites is mainly because they show frequent polymorphism, codominant inheritance, high reproducibility and high resolution, require simple typing methods, and can be detected by PCR (84).…”

Section: Microsatellitesmentioning

confidence: 99%

“…The low popularity of these genetic markers may be explained by the high number of microsatellites, which cause technical difficulties in isolating parasites by PCR (9,85).…”

Section: Microsatellitesmentioning

confidence: 99%

Molecular techniques for the study and diagnosis of parasite infection

Tavares¹,

Staggemeier²,

Borges³

et al. 2011

J. Venom. Anim. Toxins incl. Trop. Dis

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Abstract:In parasitology, routine laboratory diagnosis involves conventional methods, such as optical microscopy, used for the morphological identification of parasites. Currently, molecular biology techniques are increasingly used to diagnose parasite structures in order to enhance the identification and characterization of parasites. The objective of the present study was to review the main current and new diagnostic techniques for confirmation of parasite infections, namely: polymerase chain reaction (PCR), real-time polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), Luminex xMAP, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and restriction fragment length polymorphism (RFLP), in addition to microsatellites. Molecular assays have comprehensively assisted in the diagnosis, treatment and epidemiological studies of parasitic diseases that affect people worldwide, helping to control parasitic disease mortality.Key words: parasite infection, diagnosis, molecular techniques, molecular epidemiology. Review ARticle The Journal of Venomous Animals and Toxins including Tropical Diseases ISSN 1678-9199 | 2011 | volume 17 | issue 3 | pages 239-248 INTRODUCTIONIn parasitology, routine laboratory diagnosis involves conventional methods, such as optical microscopy, used for the morphological identification of parasites (1). However, the occasional difficulty of identifying these parasite structures may decrease the sensitivity of such methods. Currently, because of these difficulties, molecular biology has been employed to detect parasites responsible for parasitic diseases (2).Traditional parasitological analyses have the advantage of being less costly without requiring expensive reagents and equipment. Additionally, such analyses can be easily performed when a trained microscopist is available. On the other hand, molecular technology demonstrates the presence of parasites based on their antigenic components or DNA segments (3). These tests are not influenced by environmental factors that usually can interfere with the results of a stool test, for example, thus ensuring highly reliable results (4).Current laboratory diagnostic methods for the identification of parasites include: polymerase chain reaction (PCR), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), microsatellite marker method, Luminex xMAP-based technology (areas of multianalyte profiling), loop-mediated isothermal amplification (LAMP), and the recently added real-time PCR (5-12).The objective of the present article was to review the applications of molecular biology techniques in parasitology by evaluating and discussing their uses and benefits. MOLECULAR METHODS FOR DETECTION OF PARASITE STRUCTURESSeveral molecular tests to detect parasites have been developed in the last decade. Their specificity and sensitivity have gradually increased, and parasites that were previously difficult to diagnose usi...

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Abundant variation in microsatellites of the parasitic nematode Trichostrongylus tenuis and linkage to a tandem repeat

Cited by 46 publications

References 61 publications

Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data

Maximum-Likelihood Estimation of Allelic Dropout and False Allele Error Rates From Microsatellite Genotypes in the Absence of Reference Data

Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent

Molecular techniques for the study and diagnosis of parasite infection

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