Since retiring from Springdale High School in Springdale, Arkansas, where he taught world history and anthropology, he volunteers with the Arkansas Archeological Survey and the University of Arkansas Museum Collections. Rees has published articles in several books and journals on topics ranging from traditional Methodist camp meetings to music archeology. In the s and s there were a relatively small number of bluff shelter sites excavated by professional archaeologists across the Ozark Plateau region.
This article has been cited by other articles in PMC. Abstract Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes.
However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms.
Results Using MsatFinder, the total numbers of bp perfect microsatellites detected in the complete genomes of five nematode species Brugia malayi, Caenorhabditis elegans, M. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes.
Overall, AT n, AG n and CT n were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. A particular attention was paid to the microsatellite content of the plant-parasitic species M.
In this species, a repertoire of 4, microsatellite loci was identified, from which 2, appeared suitable to design markers for population genetic studies.
When compared against the InterPro domain database, of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of two closely related Meloidogyne species.
Background Microsatellites, also known as simple sequence repeats, are base pair bp nucleotide motifs tandemly repeated in the genome of every eukaryotic organism analyzed so far.
In contrast to non-repetitive DNA, microsatellite polymorphism is primarily due to variation in the number of repeated motifs rather than to substitutions. A very high mutation rate - from to mutation per microsatellite and per generation [ 1 ]- is usually associated with microsatellite loci, resulting in high heterozygosity and the presence of multiple alleles at a given locus [ 2 ].
These markers are co-dominant, abundant in non coding regions of the genome, are relatively easy to isolate, can be specifically amplified by PCR, and evolve according to mutation models that are well described [ 12 ].
Therefore, microsatellites have emerged as the most popular and versatile neutral markers for geneticists working on a wide range of topics including, among others, forensics, genome mapping, population structure, phylogeny, linkage and kinship relationships [ 3 ].
The most conventional procedure for the isolation of microsatellite markers, i. Such enrichment methods also generally use one or a few specific repeated motifs that are most often selected without prior knowledge of their abundance in the genome and may not produce suboptimal results.
The recent availability of huge amount of sequence data for a wide range of organisms, together with new methodological developments of in silico mining of microsatellites, have tremendously increased the characterization of these markers [ 5 ], and will certainly catalyze the study of genomic distribution of microsatellites in eukaryotes.
The isolation of microsatellites as useable markers appears to be more difficult in some taxa than in others, and has proved to be difficult in many invertebrates, including nematodes [ 67 ].
Except for the model species Caenorhabditis elegans, whose genome has been sequenced in the past decade [ 8 ], no genome-wide survey of microsatellites is available for nematodes.
In addition, there have been relatively few studies of microsatellites isolated by conventional molecular biology approaches in this phylum compared to other eukaryotes, e.
Such unpopularity of microsatellites as genetic markers in nematodes was attributed in part to the unusually high proportion of loci that fail to produce interpretable PCR patterns, possibly as the result of inter-locus flanking sequence similarity [ 9 ].
The root-knot nematode RKN Meloidogyne incognita is a serious plant parasite characterized by both its world-wide distribution and its very large host range [ 10 ], which raise questions about the origin, the processes of dispersal and the resulting genetic structure of the populations.
In recent years, studies of genetic diversity have been carried out in this mitotic parthenogenetic organism using neutral molecular markers such as RAPD or AFLP, and revealed rather unexpected levels of clonal diversity among populations [ 11 ]. But surprisingly, like in other nematodes, microsatellites, which are usually regarded as among the most appropriate tools to study variation at the individual level, have been very poorly investigated in this taxon.
The recent completion of genome sequencing projects has provided new opportunities to evaluate and compare the distribution of microsatellites in nematodes. Besides the genome of C. Based on these genomic resources, we report here the first survey and comparative analysis of microsatellites in nematodes, which reveal variable patterns of microsatellite abundance and diversity in the genomes of these organisms.
A more detailed focus on the genome of the RKN M. Results Relative abundance and diversity of microsatellites in nematode genomes We examined the distribution of perfect bp microsatellites using an optimized detection threshold of 12, 8, 5, 5, 5 and 5 repeats for mono- di- tri- tetra- penta- and hexa-nucleotide motifs, respectively.
For each motif type, these are the minimum number of repeats required for a microsatellite to be reported, that have been optimized as default parameters of the software to eliminate repeats which might be observed by chance [ 16 ].
So the results described here apply to microsatellites meeting this criterion. Accordingly, the total numbers of microsatellites found in the five nematode genomes appeared highly variable, ranging from 2, to 61, and covered from 0.
When considering density and coverage of the microsatellites i. The first one comprised the two RKN species, M.
The second group combined C.The survey found some surprising tendencies among the population. We conducted an opinion survey on the issue and found that most people agree.
a survey on American drinking habits Surveys of each department were conducted earlier this year. A survey of recent corporate layoffs reveals a new trend in business management.
Survey and analysis of crystal polymorphism in organic structures. Edited by M. Eddaoudi, King Abdullah University, Saudi Arabia (Received 23 October ; accepted 10 January ; online 25 January ) and it serves as the basis for the analysis herein. Technical Communication: Survey and analysis of commercial cellulase preparations suitable for biomass conversion to ethanol R.A.
Nieves, C.I. Ehrman, W.S. Adney, R.T. eBook VersionYou will receive access to this electronic text via email after using the shopping cart above to complete your purchase.4th Edition Now Available! Chicano Studies is an anthology that will begin your journey of introduction into the field of Chicano Studies as an academic discipline that for the last thirty years has sought to tell the story of Chicanos in the.
Mobile edge computing, Fog et al.: A survey and analysis of security threats and challenges. Survey and Analysis of Current Mobile Learning Applications and Technologies.
This article provides a critical analysis of m-learning projects and related literature, presenting the findings.