Evolution of a triplet repeat in a conifer

Sokol, Kerry Ann; Williams, Claire G.

doi:10.1139/g05-004

Cited by 7 publications

(5 citation statements)

References 44 publications

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“…Although the idea of an MS threshold has been investigated by numerous studies and approaches, a consensus on its existence, exact value(s), and differences across TRs of different motifs is yet to be reached (Jurka and Pethiyagoda 1995; Messier et al 1996; Bell and Jurka 1997; Cox and Mirkin 1997; Dechering et al 1998; Field and Wills 1998; Rose and Falush 1998; Dieringer and Schlotterer 2003; Lai and Sun 2003). Moreover, several studies offered evidence of slippage and slippage-like processes contributing to expansions and contractions of very STRs (Zhu et al 2000; Dieringer and Schlotterer 2003; Messer and Arndt 2007), which has led some investigators to question the very notion of an MS threshold (Pupko and Graur 1999; Noor et al 2001; Sokol and Williams 2005; Leclercq et al 2010). Although slippage does occur at very STRs, its rate at such repeats is extremely low (Kunkel 1990; Eckert et al 2002; Garcia-Diaz and Kunkel 2006).…”

Section: Introductionmentioning

confidence: 99%

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

Ananda

Walsh

Jacob

et al. 2012

Genome Biology and Evolution

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A tandem repeat’s (TR) propensity to mutate increases with repeat number, and can become very pronounced beyond a critical boundary, transforming it into a microsatellite (MS). However, a clear understanding of the mutational behavior of different TR classes and motifs and related mechanisms is lacking, as is a consensus on the existence of a boundary separating short TRs (STRs) from MSs. This hinders our understanding of MSs’ mutational properties and their effective use as genetic markers. Using indel calls for 179 individuals from 1000 Genomes Pilot-1 Project, we determined polymorphism incidence for four major TR classes, and formalized its varying relationship with repeat number using segmented regression. We observed a biphasic regime with a transition from a faster to a slower exponential growth at 9, 5, 4, and 4 repeats for mono-, di-, tri-, and tetranucleotide TRs, respectively. We used an in vitro mutagenesis assay to evaluate the contribution of strand slippage errors to mutability. STRs and MSs differ in their absolute polymorphism levels, but more importantly in their rates of mutability growth. Although strand slippage is a major factor driving mononucleotide polymorphism incidence, dinucleotide polymorphism incidence is greater than that expected due to strand slippage alone, indicating that additional cellular factors might be driving dinucleotide mutability in the human genome. Leveraging on hundreds of human genomes, we present the first comprehensive, genome-wide analysis of TR mutational behavior, encompassing several motif sizes and compositions.

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Section: Introductionmentioning

confidence: 99%

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

Ananda

Walsh

Jacob

et al. 2012

Genome Biology and Evolution

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“…From a molecular perspective, the threshold length would result from the minimum length of repeated sequences allowing stable misalignment and therefore DNA slippage. Other authors have proposed a more continuous version of this general model, suggesting that slippage occurs even at very short STRs, although at a reduced rate (Pupko and Graur 1999; Noor et al 2001; Sokol and Williams 2005). Under this scenario, there is no threshold.…”

Section: Introductionmentioning

confidence: 99%

“…Comparing homologous loci across related species with known evolutionary relationships, this approach has been extensively used to analyze the dynamics of long STRs (Richard and Dujon 1996; Angers and Bernatchez 1997; Dettman and Taylor 2004). The approach has also demonstrated that tandem duplications occur at STR loci shorter than eight nucleotides in swallows (Primmer and Ellegren 1998), fruit flies (Noor et al 2001), and conifers (Sokol and Williams 2005). These outcomes were interpreted as a result of DNA slippage.…”

Section: Introductionmentioning

confidence: 99%

DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

Leclercq¹,

Rivals²,

Jarne³

2010

Genome Biology and Evolution

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The dynamics of microsatellite, or short tandem repeats (STRs), is well documented for long, polymorphic loci, but much less is known for shorter ones. For example, the issue of a minimum threshold length for DNA slippage remains contentious. Model-fitting methods have generally concluded that slippage only occurs over a threshold length of about eight nucleotides, in contradiction with some direct observations of tandem duplications at shorter repeated sites. Using a comparative analysis of the human and chimpanzee genomes, we examined the mutation patterns at microsatellite loci with lengths as short as one period plus one nucleotide. We found that the rates of tandem insertions and deletions at microsatellite loci strongly deviated from background rates in other parts of the human genome and followed an exponential increase with STR size. More importantly, we detected no lower threshold length for slippage. The rate of tandem duplications at unrepeated sites was higher than expected from random insertions, providing evidence for genome-wide action of indel slippage (an alternative mechanism generating tandem repeats). The rate of point mutations adjacent to STRs did not differ from that estimated elsewhere in the genome, except around dinucleotide loci. Our results suggest that the emergence of STR depends on DNA slippage, indel slippage, and point mutations. We also found that the dynamics of tandem insertions and deletions differed in both rates and size at which these mutations take place. We discuss these results in both evolutionary and mechanistic terms.

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“…Examining patterns of diversity for locus 11A4D, we can see stages in the ''life cycle'' of a microsatellite locus (Zhu et al 2000;Sokol and Williams 2005). Figure 5 illustrates changes in repeat number and the number of alleles along the divergences of species as inferred from the mtDNA phylogeny.…”

Section: Discussionmentioning

confidence: 99%

“…In part, this is because there is not yet consensus on the mechanisms that underlie the high degree of polymorphism seen at many microsatellite loci (Jarne and Lagoda 1996;Goldstein and Pollock 1997;Ellegren 2000;Schlo ¨tterer 2000). Although there have been a number of attempts to reconstruct phylogenies between closely related organisms using microsatellite loci (e.g., Roy et al 1994;Harr et al 1998;Petren et al 1999;Muir et al 2000;Ritz et al 2000;Uphyrkina et al 2001;Rout et al 2008), only a few studies have used data from wild species to investigate changes in microsatellite loci at the sequence level over evolutionary time (Ross et al 2003;Sokol and Williams 2005;Ochieng et al 2007).…”

mentioning

confidence: 99%

Evolution of Microsatellite Loci in the Adaptive Radiation of Hawaiian Honeycreepers

Eggert

Beadell

McClung

et al. 2009

Journal of Heredity

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Previous studies have examined germ-line mutations to infer the processes that generate and maintain variability in microsatellite loci. Few studies, however, have examined patterns to infer processes that act on microsatellite loci over evolutionary time. Here, we examine changes in 8 dinucleotide loci across the adaptive radiation of Hawaiian honeycreepers. The loci were found to be highly variable across the radiation, and we did not detect ascertainment bias with respect to allelic diversity or allele size ranges. In examining patterns at the sequence level, we found that changes in flanking regions, repeat motifs, or repeat interruptions were often shared between closely related species and may be phylogenetically informative. Genetic distance measures based on microsatellites were strongly correlated with those based on mitochondrial DNA (mtDNA) sequences as well as with divergence time up to 3 My. Phylogenetic inferences based on microsatellite genetic distances consistently recovered 2 of the 4 honeycreeper clades observed in a tree based on mtDNA sequences but differed from the mtDNA tree in the relationships among clades. Our results confirm that microsatellite loci may be conserved over evolutionary time, making them useful in population-level studies of species that diverged from the species in which they were characterized as long as 5 Ma. Despite this, we found that their use in phylogenetic inference was limited to closely related honeycreeper species.

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Evolution of a triplet repeat in a conifer

Cited by 7 publications

References 44 publications

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

Evolution of Microsatellite Loci in the Adaptive Radiation of Hawaiian Honeycreepers

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