Microsatellites: simple sequences with complex evolution

Ellegren, Hans

doi:10.1038/nrg1348

Cited by 1,957 publications

(1,961 citation statements)

References 130 publications

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“…Microsatellites (STR) have a high mutation rate and the addition of one repetition unit is usually the most frequent one. 37 Therefore, the only factor necessary to explain this convergent evolution is the mechanism of microsatellite mutation, by which the same allele may arise independently more than once.…”

Section: Discussionmentioning

confidence: 99%

High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3

et al. 2008

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MICA is a nonclassical polymorphic MHC molecule. We investigated MICA allelic frequencies and MICA-HLA-B-HLA-C haplotypes in Brazilian Amerindians to describe the polymorphism and to extract information about the evolution of MICA gene. Kaingang is the first population described to have a high frequency of MICA*020, found associated with HLA-B*3505-HLACw*0401. Allele MICA*020 probably originated de novo in South America. The Guarani population had high frequencies of MICA*027. Allele MICA*00801 is common worldwide but rare among Amerindians, occurring only because of gene flow. The analysis of the 64 described MICA alleles revealed that in exons 2 and 4, synonymous substitutions are in excess, a result compatible with purifying selection. The opposite was observed for exons 3 and 6 and the excess of nonsynonymous substitutions was significant for exon 3, indicating positive selection. Few of the alleles described so far had exon 6 sequenced, impeding conclusions for the corresponding portion of the molecule. The analysis of the entire gene is required for a better understanding of the evolution of MICA's polymorphism and its functional consequences. This knowledge is of prime importance in view of the increasing awareness of the functional and medical implications of MICA gene variability.

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Section: Discussionmentioning

confidence: 99%

High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3

et al. 2008

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“…1995; Nadir et al. 1996; Wilder and Hollocher 2001) although it is also possible that transposable element insertion could be favored at sites containing pre‐existing microsatellites (Ellegren 2004). Regardless of their exact provenance, microsatellites associated with repetitive elements will exist in multiple copies in the genome where they will have similar or near identical flanking sequences (Zhang 2004).…”

Section: Introductionmentioning

confidence: 99%

High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

Shah

Schielzeth

Albersmeier

et al. 2016

Ecology and Evolution

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Despite recent advances in high‐throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club‐legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired‐end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild‐caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high‐throughput sequencing and graph‐based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes.

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“…The mutation rate at a microsatellite is known to depend on the intrinsic features, including repeat number, length and motif size. 29 For example, microsatellites with greater number of repeats showed higher mutation rates due to the increased probability of slippage. 30 In contrast, interruption of perfect repeat array had a great impact on the stability of microsatellite alleles.…”

Section: Discussionmentioning

confidence: 99%

Complex divergence at a microsatellite marker C1_2_5 in the lineage of HLA-Cw/-B haplotype

et al. 2009

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The human leukocyte antigen (HLA) complex locus has shaped a framework for evolutionary processes because of the dense clustering and strong linkage disequilibrium (LD) of polymorphic genes. Although the landscape of LD among conventional single-nucleotide polymorphisms (SNPs) has been described, the data on the lineage of major histocompatibility complex (MHC) haplotype are limited to pairwise comparisons of several haplotypes in Caucasoid populations. Multi-allelic markers, including microsatellite markers, may provide us with a larger power to analyze the MHC haplotype lineage because the mutation rate of microsatellite exceeds that of SNPs by several orders of magnitude. In this study, we investigated the complex structure of repeat motifs in a microsatellite to figure out the structural lineage of HLA-Cw/-B segments in Japanese. It was found that the genetic differences of HLA-Cw/-B haplotype lineage were reflected by repeat motif patterns at C1_2_5 locus, suggesting that unique mutational dynamics of microsatellites may be a useful marker to chase the haplotype lineage.

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Microsatellites: simple sequences with complex evolution

Cited by 1,957 publications

References 130 publications

High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3

High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3

High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

Complex divergence at a microsatellite marker C1_2_5 in the lineage of HLA-Cw/-B haplotype

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Microsatellites: simple sequences with complex evolution

Cited by 1,957 publications

References 130 publications

High frequencies of alleles MICA*020 and MICA*027 in Amerindians and evidence of positive selection on exon 3

High frequencies of alleles MICA*020 and MICA*027 in Amerindians and evidence of positive selection on exon 3

High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

Complex divergence at a microsatellite marker C1_2_5 in the lineage of HLA-Cw/-B haplotype

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High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3

High frequencies of alleles MICA020 and MICA027 in Amerindians and evidence of positive selection on exon 3