Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes DOI Creative Commons
Denis Roze

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 25, 2022

ABSTRACT Sex and recombination can affect the dynamics of transposable elements (TEs) in various ways: while sex is expected to help TEs spread within populations, deleterious effect ectopic among transposons represents a possible source purifying selection limiting their number. Furthermore, may also increase efficiency against by reducing selective interference loci. In order better understand effects reproductive systems on TE dynamics, this article provides analytical expressions for linkage disequilibrium (LD) classical model which number stabilized synergistic selection. The results show that positive LD predicted infinite populations despite negative epistasis, due transposition process. Positive substantial inflate variance per genome case partially selfing or clonal populations. Finite population size tends generate (Hill-Robertson effect), relative importance increasing with degree then extended explore how recombination. While generated generally disfavors recombination, Hill-Robertson represent non-negligible indirect when are abundant. However, direct fitness cost imposed drives towards low-recombination regimes, at cannot be maintained stable equilibrium.

Language: Английский

Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes DOI Open Access
Denis Roze

Genetics, Journal Year: 2023, Volume and Issue: 224(2)

Published: April 6, 2023

Abstract Sex and recombination can affect the dynamics of transposable elements (TEs) in various ways: while sex is expected to help TEs spread within populations, deleterious effect ectopic among transposons represents a possible source purifying selection limiting their number. Furthermore, may also increase efficiency against by reducing selective interference loci. In order better understand effects reproductive systems on TE dynamics, this article provides analytical expressions for linkage disequilibrium classical model which number stabilized synergistic selection. The results show that positive predicted infinite populations despite negative epistasis, due transposition process. Positive substantially inflate variance per genome case partially selfing or clonal populations. Finite population size tends generate (Hill–Robertson effect), relative importance increasing with degree then extended explore how recombination. While generated generally disfavors recombination, Hill–Robertson represent non-negligible indirect when are abundant. However, direct fitness cost imposed drives towards low-recombination regimes, at cannot be maintained stable equilibrium.

Language: Английский

Citations

19
Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA based host defense against invadingP-elements DOI Creative Commons
Divya Selvaraju, Filip Wierzbicki, Robert Kofler

et al.

Genome Research, Journal Year: 2024, Volume and Issue: unknown

Published: March 15, 2024

To prevent the spread of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major mechanism operates through PIWI-interacting RNAs (piRNAs). investigate establishment host defense, we introduced P -element, one most widely studied eukaryotic transposons, into naive lines Drosophila erecta . We monitored invasion in three replicates for more than 50 generations by sequencing genomic DNA (using short long reads), small RNAs, transcriptome at regular intervals. A piRNA-based was rapidly established two (R1, R4) but not third (R2), which -element copy numbers kept increasing over generations. found that ping-pong cycle could be activated R2, although is fully functional against other TEs. Furthermore, R2 had both insertions piRNA clusters siRNAs, suggesting neither them sufficient to trigger defense. Our work shows control an invading TE requires activation this stochastic event may fail some populations, leading proliferation TEs ultimately threaten integrity genome.

Language: Английский

Citations

5
On the origin of the P-element invasion in Drosophila simulans DOI Creative Commons
Filip Wierzbicki, Riccardo Pianezza, Divya Selvaraju

et al.

Mobile DNA, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 26, 2025

Language: Английский

Citations

0
The impact of paramutations on the invasion dynamics of transposable elements DOI Creative Commons

Almorò Scarpa,

Robert Kofler

Genetics, Journal Year: 2023, Volume and Issue: 225(4)

Published: Oct. 11, 2023

According to the prevailing view, trap model, activity of invading transposable elements (TEs) is greatly reduced when a TE copy jumps into piRNA cluster, which triggers emergence piRNAs that silence TE. One crucial component in host defence are paramutations. Mediated by maternally deposited piRNAs, paramutations convert insertions producing loci, thereby transforming selfish TEs agents defence. Despite this significant effect, impact on dynamics invasions remains unknown. To address issue, we performed extensive forward simulations with clusters and We found significantly affect dynamics, accelerating silencing invasions, reducing number accumulating during mitigating fitness cost TEs. also demonstrate production induced paramutations, an epigenetically inherited trait, may be positively selected. Finally, show account for three important open problems model. Firstly, paramutated compensate insufficient observed previous studies. Secondly, explain discrepancy between expected abundance different families Drosophila melanogaster. Thirdly, trigger defence, but render dispensable once has been established. This could lack activation major were deleted study.

Language: Английский

Citations

7
The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model DOI Creative Commons
Filip Wierzbicki, Robert Kofler

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: Oct. 20, 2023

Abstract Background It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates stopped when copy TE jumps into piRNA cluster (i.e., trap model). However, recent works, which for example showed deletion three major clusters has no effect on activity, cast doubt model. Results Here, we test model from population genetics perspective. Our simulations show composition regions act as transposon traps potentially clusters) ought to deviate have activity. We investigated TEs five Drosophila melanogaster strains using complementary approaches whether matches these expectations. found abundance families inside outside highly correlated, although this not expected under Furthermore, distribution number insertions also much broader than expected. Conclusions observed agreement with expectations simple Dispersed producing temporal well spatial heterogeneity may account deviations.

Language: Английский

Citations

7
Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s DOI Creative Commons
Riccardo Pianezza,

Almorò Scarpa,

Prakash Narayanan

et al.

PLoS Genetics, Journal Year: 2024, Volume and Issue: 20(3), P. e1011201 - e1011201

Published: March 26, 2024

During the last few centuries D. melanogaster populations were invaded by several transposable elements, most recent of which was thought to be P -element between 1950 and 1980. Here we describe a novel TE, named Spoink , that has . It is 5216nt LTR retrotransposon Ty3/gypsy superfamily. Relying on strains sampled at different times during century show worldwide after 1983 1993. This invasion likely triggered horizontal transfer from willistoni group, much as -element. probably silenced piRNA pathway in natural about 1/3 examined have an insertion into canonical cluster such 42AB Given degree genetic investigation it perhaps surprising able invade unnoticed.

Language: Английский

Citations

2
Unveiling the complete invasion history ofD. melanogaster: three horizontal transfers of transposable elements in the last 30 years DOI
Riccardo Pianezza,

Almorò Scarpa,

Anna Haider

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 28, 2024

Abstract Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting significant influence on evolution throughout the tree life. Using a novel approach that does not require prior knowledge about sequence repeats, we identified three TE invasions in D. melanogaster : MLE spread between 1990-2000, Souslik 2009-2012, and Transib1 2013-2016. We recapitulate findings, revealing total 11 TEs invaded over past two centuries. Leveraging data from 1400 arthropod provide evidence were triggered by horizontal transfers, with simulans species willistoni group acting as putative donors. Through analysis ∼ 600 short-read datasets spanning diverse geographic regions, reveal rapidity invasions: swiftly multiplied isolated epicenters 2014 to all investigated populations just years. Our findings suggest anthropogenic activities, facilitating habitat population expansions , might have accelerated rate transposon transfer well into worldwide population. Given impact genomes potential involvement humans their dispersal, our research has crucial implications for both ecology.

Language: Английский

Citations

2
The composition of piRNA clusters inDrosophila melanogasterdeviates from expectations under the trap model DOI Creative Commons
Filip Wierzbicki, Robert Kofler

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 15, 2023

Abstract It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates stopped when copy TE jumps into piRNA cluster (i.e. trap model). However, recent works, which for example showed deletion three major clusters has no effect on activity, cast doubt model. Therefore, we aim to test We show with population genetic simulations composition regions act as transposon traps possible clusters) ought deviate from have activity. Next, investigated TEs five D. melanogaster strains using complementary approaches whether matches these expectations. found abundance families inside outside highly correlated, although this not expected under Furthermore, distribution number insertions also much broader than expected, where some zero others more 14. One feasible explanation little activity model therefore incorrect. Alternatively, dispersed producing temporal well spatial heterogeneity may explain our observations.

Language: Английский

Citations

5
A population genetics theory for piRNA-regulated transposable elements DOI Creative Commons
Siddharth S. Tomar, Aurélie Hua‐Van, Arnaud Le Rouzic

et al.

Theoretical Population Biology, Journal Year: 2023, Volume and Issue: 150, P. 1 - 13

Published: March 1, 2023

Language: Английский

Citations

4
Spoink, a LTR retrotransposon, invadedD. melanogasterpopulations in the 1990s DOI Creative Commons
Riccardo Pianezza,

Almorò Scarpa,

Prakash Narayanan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 2, 2023

Abstract During the last few centuries D. melanogaster populations were invaded by several transposable elements, most recent of which was thought to be P -element between 1950 and 1980. Here we describe a novel TE, named Spoink , that has . It is 5216nt LTR retrotransposon Ty3/gypsy superfamily. Relying on strains sampled at different times during century show worldwide after 1983 1993. This invasion likely triggered horizontal transfer from willistoni group, much as -element. probably silenced piRNA pathway in natural about 1/3 examined have an insertion into canonical cluster such 42AB Given degree genetic investigation it surprising able invade unnoticed.

Language: Английский

Citations

3