Hypervariability of simple sequences as a general source for polymorphic DNA markers

Tautz, Diethard

doi:10.1093/nar/17.16.6463

Cited by 1,972 publications

(1,144 citation statements)

References 28 publications

(18 reference statements)

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“…Microsatellites were identified according to the protocol of Tautz (1989), and polymerase chain reaction (PCR) primers were designed for clones containing at least eight repeats. These primers were used to amplify samples of gag DNA to identify those loci that contained sufficient polymorphism to meet the study objectives.…”

Section: Methodsmentioning

confidence: 99%

Stock Identification of Gag, Mycteroperca microlepis, Along the Southeast Coast of the United States

et al. 1999

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Abstract:The gag grouper Mycteroperca microlepis is an important component of commercial and recreational fisheries along the South Atlantic coast of the United States and in the Gulf of Mexico. Over the past two decades, this species has experienced significant declines in abundance and an increasing skew in sex ratios.Analysis of microsatellite DNA variation in this species shows mosaic patterns of population subdivision and significant departures from Hardy-Weinberg equilibrium in all sampling locations. Given the length of the pelagic stage (egg and larvae), the prevailing current patterns, and the migratory capabilities of the adults, it is unlikely that these observations are the result of restricted gene flow among genetically differentiated populations. The apparent structure of gag populations most likely reflects inbreeding in size-limited populations.Population declines, skewed sex ratios, and perhaps variance in female fecundity appear to have acted in concert to limited the number of individuals that contribute to a given year class. These data are reinforced by studies of other fish stocks that have experienced precipitous declines over the past two decades.

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Section: Methodsmentioning

confidence: 99%

Stock Identification of Gag, Mycteroperca microlepis, Along the Southeast Coast of the United States

et al. 1999

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“…Microsatellites are polymorphic DNA sequences containing short tandemly arranged repetitions [10], distributed throughout the genome, and found in all prokaryotic and eukaryotic genomes [11]. Due to their high variability, these genetic markers have been widely used in genetic mapping [12] and population structure studies [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of microsatellite markers for the population genetic structure in endemic red-tailed barb, Gonoproktopterus curmuca

et al. 2014

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Gonoproktopterus curmuca is an endangered red tailed barb found in Southern part of Western Ghat, India. As a part of stock-specific, propagation assisted rehabilitation and management program, polymorphic microsatellites markers were used to study the genetic diversity and population structure of this species from the three River systems of Southern Western Ghats, such as Periyar River, the Chalakkudy River, and the Chaliyar River. From selected eight polymorphic microsatellite markers, the number of alleles per locus ranged from 2 to 8, and the average number of alleles among 3 populations ranged from 5.0 to 5.75. The mean observed (H ob ) and expected (H ex ) heterozygosity ranged from 0.5148 to 0.5360 and from 0.5996 to 0.6067, respectively. Significant deviations from Hardy-Weinberg Equilibrium expectation were found at majority of the loci (except Gcur MFW72 and Gcur MFW19) and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance indicates that the percent of variance among populations and within populations were 6.73 and 93.27, respectively. The pairwise F ST values between populations indicate that there were significant deviations in genetic differentiations for the red-tailed barb populations from these three Rivers of the Western Ghats, India. The microsatellites methods reported a low degree of gene diversity and lack of genetic heterogeneity in the population of G. curmuca, which strongly emphasize the need of fishery management, conservation and rehabilitation of G. curmuca.

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“…Microsatellites that originate at independent loci have unique flanking DNA that is used to design locus-specific genetic markers (Pemberton et al 1995) that are desirable due to high levels of allelic variation (Tautz 1989;Weber and May 1989). Polymorphic microsatellite markers from Lepidoptera have been used for linkage mapping (Miao et al 2005) and population genetic studies (Reddy et al 1999;Prasad et al 2005;Malausa et al 2007), but problems often arise during genotype analyses.…”

Section: Introductionmentioning

confidence: 99%

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

et al. 2010

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Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element ( MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains. Abstract Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A ? T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA) n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA) n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA) n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA) n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.

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Hypervariability of simple sequences as a general source for polymorphic DNA markers

Cited by 1,972 publications

References 28 publications

Stock Identification of Gag, Mycteroperca microlepis, Along the Southeast Coast of the United States

Stock Identification of Gag, Mycteroperca microlepis, Along the Southeast Coast of the United States

Identification and characterization of microsatellite markers for the population genetic structure in endemic red-tailed barb, Gonoproktopterus curmuca

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

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