scholarly journals Accumulation of transposable elements in selfing populations of Arabidopsis lyrata supports the ectopic recombination model of transposon evolution

2018 ◽  
Vol 219 (2) ◽  
pp. 767-778 ◽  
Author(s):  
Georgi Bonchev ◽  
Yvonne Willi
Keyword(s):  
Transposable Elements ◽  
Arabidopsis Lyrata ◽  
Ectopic Recombination ◽  
Recombination Model ◽  
Transposon Evolution

scholarly journals Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

2011 ◽  
Vol 108 (6) ◽  
pp. 2322-2327 ◽  
Author(s):  
J. D. Hollister ◽  
L. M. Smith ◽  
Y.-L. Guo ◽  
F. Ott ◽  
D. Weigel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transposable Elements ◽  
Small Rnas ◽  
Expression Divergence ◽  
Gene Expression Divergence ◽  
Arabidopsis Lyrata

Methylation of repeated DNA sequences and genome stability in Ascobolus immersus

1995 ◽  
Vol 73 (S1) ◽  
pp. 221-225 ◽  
Author(s):  
Vincent Colot ◽  
Christophe Goyon ◽  
Godeleine Faugeron ◽  
Jean-Luc Rossignol
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Genome Stability ◽  
Methylation Status ◽  
Biological Significance ◽  
Dna Repeats ◽  
Repeated Dna ◽  
Key Words Dna ◽  
Ectopic Recombination ◽  
Ascobolus Immersus

In the ascomycete Ascobolus immersus, artificially repeated DNA fragments are subject to a process of methylation induced premeiotically (MIP). Artificially repeated genes are inactivated as a consequence of this methylation. Once established, both methylation and inactivation are stably maintained (although they can be reversed) through vegetative as well as sexual reproduction, even after the different copies of the repeat have segregated from each other. Therefore, MIP constitutes a process of epimutation. The biological significance of MIP remains unknown. Two likely hypotheses, which are not mutually exclusive, are that MIP acts to limit the spread of transposable elements throughout the genome or that it acts to reduce ectopic recombination between dispersed sequences. In this second hypothesis, targets for MIP are also likely to be mainly transposable elements. For these reasons, we have recently started a search for such elements in Ascobolus. Results obtained so far indicate that several types of transposable elements or remnants of them are present in Ascobolus. Analysis of their methylation status suggests that they are indeed likely targets of MIP and in one case points to a possible strategy that transposons might use to escape MIP, simply by reducing their size. Key words: DNA repeats, methylation, genome stability, Ascobolus immersus.

scholarly journals Synergistic epistasis of the deleterious effects of transposable elements

2021 ◽  
Author(s):  
Grace Yuh Chwen Lee
Keyword(s):  
Transposable Elements ◽  
Copy Number ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Epistatic Interactions ◽  
Ectopic Recombination ◽  
Epigenetic Effects ◽  
Deleterious Alleles ◽  
Genetic Signal ◽  
Outstanding Question

The replicative nature and generally deleterious effects of transposable elements (TEs) give rise to an outstanding question about how TE copy number is stably contained in host populations. Classic theoretical analyses predict that, when the decline in fitness due to each additional TE insertion is greater than linear, or when there is synergistic epistasis, selection against TEs can result in a stable equilibrium of TE copy number. While several mechanisms are predicted to yield synergistic deleterious effects of TEs, we lack empirical investigations of the presence of such epistatic interactions. Purifying selection with synergistic epistasis generates repulsion linkage between deleterious alleles and, accordingly, an underdispersed distribution for the number of deleterious mutations among individuals. We investigated this population genetic signal in an African Drosophila melanogaster population and found evidence for synergistic epistasis among TE insertions, especially those expected to have large fitness impacts. Curiously, even though ectopic recombination has long been predicted to generate nonlinear fitness decline with increased TE copy number, TEs predicted to suffer higher rates of ectopic recombination are not more likely to be underdispersed. On the other hand, underdispersed TE families are more likely to show signatures of deleterious epigenetic effects and stronger ping-pong signals of piRNA amplification, a hypothesized source from which synergism of TE-mediated epigenetic effects arises. Our findings set the stage for investigating the importance of epistatic interactions in the evolutionary dynamics of TEs.

scholarly journals Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily

2019 ◽  
Vol 37 (2) ◽  
pp. 355-364
Author(s):  
Watal M Iwasaki ◽  
T E Kijima ◽  
Hideki Innan
Keyword(s):  
Population Genetics ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Copy Number ◽  
Internal Branch ◽  
Ectopic Recombination ◽  
A Genome ◽  
Different Types ◽  
Long Time ◽  
New Type

Abstract In order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.

Survey of transposable elements from rice genomic sequences

2001 ◽  
Vol 25 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Kime Turcotte ◽  
Sujatha Srinivasan ◽  
Thomas Bureau
Keyword(s):  
Transposable Elements ◽  
Genomic Sequences

The utility of transposable elements as tools for the isolation of plant genes

1990 ◽  
Vol 79 (1) ◽  
pp. 105-115 ◽  
Author(s):  
Joel M. Chandlee
Keyword(s):  
Transposable Elements ◽  
Plant Genes
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