Microsatellites in different eukaryotic genomes: survey and analysis.

By G. Tóth, Zoltán Gáspári, Jerzy Jurka. Genome Research, 2000

1,481 citations recorded by the source corpus.

We examined the abundance of microsatellites with repeated unit lengths of 1-6 base pairs in several eukaryotic taxonomic groups: primates, rodents, other mammals, nonmammalian vertebrates, arthropods, Caenorhabditis elegans, plants, yeast, and other fungi. Distribution of simple sequence repeats was compared between exons, introns, and intergenic regions. Tri- and hexanucleotide repeats prevail in protein-coding exons of all taxa, whereas the dependence of repeat abundance on the length of the repeated unit shows a very different pattern as well as taxon-specific variation in intergenic regions and introns. Although it is known that coding and noncoding regions differ significantly in their microsatellite distribution, in addition we could demonstrate characteristic differences between intergenic regions and introns. We observed striking relative abundance of (CCG)(n)*(CGG)(n) trinucleotide repeats in intergenic regions of all vertebrates, in contrast to the almost complete lack of this motif from introns. Taxon-specific variation could also be detected in the frequency distributions of simple sequence motifs. Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/67ebc67fac8f65c80c8ae235aefa09283b5131af

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Citations in the corpus

Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR (2005, methodology): “Although the most frequently occuring microsatellite dinucleotide repeats in plants are (AT) (Lagercrantz et al. 1993; Wang et al. 1994; Powell et al. 1996a; Toth et al. 2000 ), we decided to develop microsatellite markers containing (CT)/ (AG) and (CA)/(TG) repeats in order to avoid problems in sc”
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review (2002, background): “Tóth et al. (2000) conducted a detailed analysis of SSRs in several eukaryotic taxa, from fungi to humans, and”
Potential of marker-assisted selection in hemp genetic improvement (2004, background): “It was found that the most common repeated motif, the dinucleotide GA/CT, is also the most frequently detected not only in the close relative hop, but in general in the plant kingdom (Alghanim and Almirall, 2003; Jake et al., 2001; Toth et al., 2000).”
EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera (2011, background): “They are widespread in both eukaryotic and prokaryotic genomes (Field and Wills 1998; Toth et al. 2000) and occur in both coding and noncoding regions (Powell et al. 1996a; Toth et al 2000).”
The linkage disequilibrium and the selection of genetic markers for association studies in European populations (2007, background): “Microsatellites, also referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs) are repeats of 1–6 bp units totaling < 200 bp in length (Toth et al. 2000).”
Microsatellite Markers in Plants and Insects. Part I: Applications of Biotechnology (2009, background): “…in 1981 by sequence analysis of alleles at the β globin locus (Miesfeld et al. 1981; Spritz 1981) and subsequently found to be naturally occurring and ubiquitous in prokaryotic and eukaryotic genomes (Tautz and Renz 1984; Jeffreys et al. 1985; Tautz 1989; Thoren et al. 1995; Toth et al. 2000).”
Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa (2004, background): “, computational molecular biology, of repeats and their flanking regions has recently been explored (Toth et al. 2000; Temnykh et al. 2001; Morgante et al. 2002).”
Microsatellites and their genomic distribution, evolution, function and applications : A review with special reference to fish genetics (2006, background): “5-fold less common in genomic DNA of vertebrates than dinucleotides (Toth et al., 2000).”
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, background): “Microsatellite repeats (Toth et al. 2000) and low-complexity sequence, as well as cen-”
Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes (2002, background): “Large-scale genomic and EST sequencing provides the opportunity to evaluate the abundance and relative distribution of microsatellite”
Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. (2006, background): “Trinucleotide and hexanucleotide repeats are the most likely repeat classes to appear in coding regions because they do not cause a frameshift (Toth et al. 2000).”
Origin, evolution and genome distribution of microsatellites (2006, background): “Tóth et al. (2000) reported that the total number of 1 to 6 repeat microsatellites varies depending on the taxonomic group concerned, ranging from 13,889 (approximately 429 per Mb, excluding single-base repeats) in Rodentia, to 4,139 (154 per Mb) in Embryophyta, 3,004 (99 per Mb) in Sacharomyces…”
Methods for Development of Microsatellite Markers: An Overview (2014, neutral): “Microsatellites are ubiquitous in the coding and noncoding regions (Tautz and Renz, 1984; Gupta et al., 1996; Toth et al., 2000) with a higher density of simple sequence motifs in the noncoding regions of eukaryotes (Hancock, 1995; Li et al., 2002).”