Mutability and evolvability: Indirect selection for mutability

King, David G.; Kashi, Yechezkel

doi:10.1038/sj.hdy.6800998

Cited by 14 publications

(6 citation statements)

References 11 publications

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“…The dN-dS test revealed few negatively selected sites in the triplets for each EST-SSR (Additional file 7). The positive selection in SSR based sequence was reported in other studies [8,49-51]. More than 50% of sites for both motifs analyzed across species were under a positive selection (dN/dS > 1), suggesting a weak selection pressure on these EST-SSR motifs, as was reported for other species [52,53].…”

Section: Resultssupporting

confidence: 76%

In silicocomparative analysis of SSR markers in plants

2011

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BackgroundThe adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.ResultsIn this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.ConclusionsThe comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

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Section: Resultssupporting

confidence: 76%

In silicocomparative analysis of SSR markers in plants

2011

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“…Variation within these promoter microsatellites has the potential to affect promoter function, which can ultimately lead to variation in phenotypes. This variation may be selectively beneficial [86], [87], and by targeting promoter microsatellites, especially those that are conserved [12], [71], we hope to uncover sources of human phenotypic variation.…”

Section: Resultsmentioning

confidence: 99%

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

et al. 2013

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Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context.

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“…Single amino acid repeat polymorphisms (SARPs) have been proposed as a genetic mechanism that can generate morphological variation [10,17,30,84-88]. This study provides several lines of support for these claims.…”

Section: Discussionmentioning

confidence: 63%

“…Rather than being purged from the genome, long repeats are frequently conserved across vertebrates [19,24-27] and those containing glutamine or alanine tend to occur in transcription factors [28,29]. Contraction or expansion of a codon repeat in a transcription factor has the potential to modulate gene regulation in a quantitative, rather than qualitative, manner [10,30] and, therefore, result in a mutation of small effect [22]. Thus, SARPs appear to have the potential both to generate genetic variation and to enable adaptive change in morphology.…”

Section: Introductionmentioning

confidence: 99%

Length polymorphism and head shape association among genes with polyglutamine repeats in the stalk-eyed fly, Teleopsis dalmanni

et al. 2010

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BackgroundPolymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalmanni. Using an annotated expressed sequence tag database developed from eye-antennal imaginal disc tissues in T. dalmanni we identified 98 genes containing nine or more consecutive copies of a single amino acid. We then quantify variation in length and allelic diversity for 32 codon and 15 noncodon repeat regions in a large outbred population. We also assessed the frequency with which amino acid repeats are either gained or lost by identifying sequence similarities between T. dalmanni SARP loci and their orthologs in Drosophila melanogaster. Finally, to identify SARP containing genes that may influence head development we conducted a two-generation association study after assortatively mating for extreme relative eyespan.ResultsWe found that glutamine repeats occur more often than expected by amino acid abundance among 3,400 head development genes in T. dalmanni and D. melanogaster. Furthermore, glutamine repeats occur disproportionately in transcription factors. Loci with glutamine repeats exhibit heterozygosities and allelic diversities that do not differ from noncoding dinucleotide microsatellites, including greater variation among X-linked than autosomal regions. In the majority of cases, repeat tracts did not overlap between T. dalmanni and D. melanogaster indicating that large glutamine repeats are gained or lost frequently during Dipteran evolution. Analysis of covariance reveals a significant effect of parental genotype on mean progeny eyespan, with body length as a covariate, at six SARP loci [CG33692, ptip, band4.1 inhibitor LRP interactor, corto, 3531953:1, and ecdysone-induced protein 75B (Eip75B)]. Mixed model analysis of covariance using the eyespan of siblings segregating for repeat length variation confirms that significant genotype-phenotype associations exist for at least one sex at five of these loci and for one gene, CG33692, longer repeats were associated with longer relative eyespan in both sexes.ConclusionAmong genes expressed during head development in stalk-eyed flies, long codon repeats typically contain glutamine, occur in transcription factors and exhibit high levels of heterozygosity. Furthermore, the presence of significant associations within families between repeat length and head shape indicates that six genes, or genes linked to them, contribute genetic variation to the development of this extremely sexually dimorphic trait.

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Mutability and evolvability: Indirect selection for mutability

Cited by 14 publications

References 11 publications

In silicocomparative analysis of SSR markers in plants

In silicocomparative analysis of SSR markers in plants

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

Length polymorphism and head shape association among genes with polyglutamine repeats in the stalk-eyed fly, Teleopsis dalmanni

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