scholarly journals The variable ELF3 polyglutamine tract mediates complex epistatic interactions in Arabidopsis thaliana

2016 ◽  
Author(s):  
◽  
Christine Queitsch
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Mutation Rate ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
High Mutation Rate ◽  
Hybrid Strategy ◽  
Coding Regions ◽  
Polyglutamine Tract ◽  
Short Tandem

ABSTRACTShort tandem repeats are hypervariable genetic elements that occur frequently in coding regions. Their high mutation rate readily generates genetic variation contributing to adaptive evolution and human diseases. We recently proposed that short tandem repeats are likely to engage in epistasis because they are well-positioned to compensate for genetic variation arising at other loci due to their high mutation rate. We previously reported that natural ELF3 polyglutamine variants cause reciprocal genetic incompatibilities in two divergent Arabidopsis thaliana backgrounds. Here, we dissected the genetic architecture of this incompatibility and used a yeast two-hybrid strategy to identify proteins whose physical interactions with ELF3 were modulated by polyglutamine tract length. Using these two orthogonal approaches, we identify specific genetic interactions and physical mechanisms by which the ELF3 polyglutamine tract may mediate the observed genetic incompatibilities. Our work elucidates how short tandem repeat variation, which is generally underascertained in population-scale sequencing, can contribute to phenotypic variation. Furthermore, our results support our proposal that highly variable STR loci can contribute disproportionately to the epistatic component of heritability.

scholarly journals The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time

2004 ◽  
Vol 74 (1) ◽  
pp. 50-61 ◽  
Author(s):  
Lev A. Zhivotovsky ◽  
Peter A. Underhill ◽  
Cengiz Cinnioğlu ◽  
Manfred Kayser ◽  
Bharti Morar ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Mutation Rate ◽  
Human Population ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Divergence Time ◽  
Population Divergence ◽  
Short Tandem

scholarly journals A broad mutational target explains a fast rate of phenotypic evolution

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Fabrice Besnard ◽  
Joao Picao-Osorio ◽  
Clément Dubois ◽  
Marie-Anne Félix
Keyword(s):  
Cell Fate ◽  
Mutation Rate ◽  
Tandem Repeats ◽  
Spontaneous Mutation ◽  
Rapid Evolution ◽  
High Mutation Rate ◽  
Sustained Action ◽  
Fast Evolution ◽  
Mutational Variance ◽  
Short Tandem

The rapid evolution of a trait in a clade of organisms can be explained by the sustained action of natural selection or by a high mutational variance, that is the propensity to change under spontaneous mutation. The causes for a high mutational variance are still elusive. In some cases, fast evolution depends on the high mutation rate of one or few loci with short tandem repeats. Here, we report on the fastest evolving cell fate among vulva precursor cells in Caenorhabditis nematodes, that of P3.p. We identify and validate causal mutations underlying P3.p's high mutational variance. We find that these positions do not present any characteristics of a high mutation rate, are scattered across the genome and the corresponding genes belong to distinct biological pathways. Our data indicate that a broad mutational target size is the cause of the high mutational variance and of the corresponding fast phenotypic evolutionary rate.

Short Tandem Repeats and Genetic Variation

2010 ◽  
pp. 297-306 ◽  
Author(s):  
Bo Eskerod Madsen ◽  
Palle Villesen ◽  
Carsten Wiuf
Keyword(s):  
Genetic Variation ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana

2018 ◽  
Vol 28 (8) ◽  
pp. 1169-1178 ◽  
Author(s):  
Maximilian O. Press ◽  
Rajiv C. McCoy ◽  
Ashley N. Hall ◽  
Joshua M. Akey ◽  
Christine Queitsch
Keyword(s):  
Arabidopsis Thaliana ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Functional Consequences ◽  
Short Tandem

scholarly journals Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana

2017 ◽  
Author(s):  
Maximilian O. Press ◽  
Rajiv C. McCoy ◽  
Ashley N. Hall ◽  
Joshua M. Akey ◽  
Christine Queitsch
Keyword(s):  
Arabidopsis Thaliana ◽  
Complex Traits ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Intron Retention ◽  
Purifying Selection ◽  
Genomic Variation ◽  
Functional Consequences ◽  
Short Tandem

AbstractShort tandem repeat (STR) mutations may be responsible for more than half of the mutations in eukaryotic coding DNA, yet STR variation is rarely examined as a contributor to complex traits. We assess the scope of this contribution across a collection of 96 strains of Arabidopsis thaliana by massively parallel STR genotyping. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR in these strains. Modest STR expansions are found in most strains, some of which have evident functional effects. For instance, three of six intronic STR expansions are associated with intron retention. Coding STRs are depleted of variation relative to non-coding STRs, consistent with the action of purifying selection, and some STRs show hypervariable patterns consistent with diversifying selection. Finally, we detect dozens of novel STR-phenotype associations that could not be detected with SNPs alone, validating several with follow-up experiments. Our results demonstrate that STRs comprise a large, unascertained reservoir of functionally relevant genomic variation.

scholarly journals Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution

2021 ◽  
Vol 1 ◽  
Author(s):  
Alina-Alexandra Voicu ◽  
Michael Krützen ◽  
Tugce Bilgin Sonay
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Demographic History ◽  
Population Variation ◽  
Local Adaptations ◽  
A Genome ◽  
The Impact ◽  
Short Tandem

The genus Pongo is ideal to study population genetics adaptation, given its remarkable phenotypic divergence and the highly contrasting environmental conditions it’s been exposed to. Studying its genetic variation bears the promise to reveal a motion picture of these great apes’ evolutionary and adaptive history, and also helps us expand our knowledge of the patterns of adaptation and evolution. In this work, we advance the understanding of the genetic variation among wild orangutans through a genome-wide study of short tandem repeats (STRs). Their elevated mutation rate makes STRs ideal markers for the study of recent evolution within a given population. Current technological and algorithmic advances have rendered their sequencing and discovery more accurate, therefore their potential can be finally leveraged in population genetics studies. To study patterns of population variation within the wild orangutan population, we genotyped the short tandem repeats in a population of 21 individuals spanning four Sumatran and Bornean (sub-) species and eight Southeast Asian regions. We studied the impact of sequencing depth on our ability to genotype STRs and found that the STR copy number changes function as a powerful marker, correctly capturing the demographic history of these populations, even the divergences as recent as 10 Kya. Moreover, gene ontology enrichments for genes close to STR variants are aligned with local adaptations in the two islands. Coupled with more advanced STR-compatible population models, and selection tests, genomic studies based on STRs will be able to reduce the gap caused by the missing heritability for species with recent adaptations.

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