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

Almorò Scarpa,

Robert Kofler

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

Published: March 15, 2023

Abstract According to the prevailing view, trap model, invading transposable elements (TEs) are stopped in their proliferation when a TE copy jumps into piRNA cluster, which triggers emergence of piRNAs that silence TE. One crucial component host defence 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 D. melanogaster . Thirdly, render dispensable once has been established, lack activation major were deleted study.

Language: Английский

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century DOI Creative Commons

Almorò Scarpa,

Riccardo Pianezza, Filip Wierzbicki

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 2, 2024

Transposable element invasions have a profound impact on the evolution of genomes and phenotypes. It is thus an important open question how often such TE occur. To address this question, we utilize historical specimens, sampled about 200 y ago. We found that LTR retrotransposons Blood, Opus, 412 spread in Drosophila melanogaster 19th century. These constitute second waves, as degraded fragments were for all three TEs. The composition Opus 412, but not shows pronounced geographic heterogeneity, likely due to founder effects during invasions. Finally, identified species from simulans complex origin show total, seven families invaded D. last 200y, thereby increasing genome size by up 1.2Mbp. suggest high rate was triggered human activity. Based analysis strains specimens at different times, provide detailed timeline invasions, making first organism where invasion history TEs two centuries could be inferred.

Language: Английский

Citations

7
Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19thcentury DOI Creative Commons

Almorò Scarpa,

Riccardo Pianezza, Filip Wierzbicki

et al.

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

Published: June 8, 2023

Abstract Transposable element invasions have a profound impact on the evolution of genomes and phenotype. It is thus an important open question how often such TE occur. Based strains sampled at different times, previous work showed that four families invaded D. melanogaster during 20 th century. Here we utilize historical specimens to extend this by another 100 years. We found LTR retrotransposons Blood, Opus 412 spread in 19 These were constitute second waves, as degraded fragments for all three TEs. show two invasions, 412, led pronounced geographic heterogeneity, likely due founder effects invasions. Finally, identified species from simulans complex origin In total, seven last 200 years, increasing genome size 1.2 Mbp. analysis provide detailed timeline making first organism where could infer invasion history TEs centuries.

Language: Английский

Citations

6
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
The impact of insertion bias into piRNA clusters on the invasion of transposable elements DOI Creative Commons

Shashank Pritam,

Almorò Scarpa,

Robert Kofler

et al.

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

Published: Oct. 6, 2024

Abstract In our current understanding of transposable element (TE) invasions TEs move freely until they accidentally insert into a piRNA cluster. They are then silenced by the production cognate to TE. Under this model, one would expect that might evolve avoid clusters. Yet empirical observations show some TEs, such as P -element, clusters preferentially. We were thus wondering if bias could be beneficial for TE, example minimizing harm host while still being able selfishly spread in populations. decided model insertion determine there was ever situation which performed extensive forward simulations TE with differing biases found significantly altered invasion dynamics primarily changing copy number individuals prior silencing. Insertion cluster reduced deleterious effects population, but we avoiding out-compete towards insertions. only when negative selection against and lack recombination. Different different suggesting an attribute not host, yet scenarios is quite limited. This opens up interesting area future research during invasions. Significance Statement study challenges pre-existing investigating potential adaptive role Using simulations, demonstrate alters dynamics, it generally TE’s Our results also elements (TEs) tend do better than those more likely preferencially these work provides novel insights complex between genomes, showing limited where advantageous TEs. These open new evolution host-TE interactions, further contributing genome stability.

Language: Английский

Citations

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

Almorò Scarpa,

Robert Kofler

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

Published: March 15, 2023

Abstract According to the prevailing view, trap model, invading transposable elements (TEs) are stopped in their proliferation when a TE copy jumps into piRNA cluster, which triggers emergence of piRNAs that silence TE. One crucial component host defence 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 D. melanogaster . Thirdly, render dispensable once has been established, lack activation major were deleted study.

Language: Английский

Citations

1