Tirant stealthily invaded natural<i>Drosophila melanogaster</i>populations during the last century

Schwarz, Florian; Wierzbicki, Filip; Senti, Kirsten-André; Kofler, Robert

doi:10.1101/2020.06.10.144378

Cited by 4 publications

(1 citation statement)

References 131 publications

(179 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…TE invasions could be much more abundant than previously assumed. For example, at least 8 different TEs invaded the genome of D. melanogaster during the last 200 years (Scarpa et al, 2024). TE invasions could thus pose a persistent threat to genome integrity of organisms.…”

Section: Consequences For Natural Populationsmentioning

confidence: 99%

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Selvaraju,

Wierzbicki,

Kofler

2024

Genome Res.

View full text Add to dashboard Cite

To prevent the spread of transposable elements (TEs) hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defence we introduced theP-element, one of the most widely studied eukaryotic transposons, into naive lines ofDrosophila erecta. We monitored the invasion in 3 replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs and the transcriptome at regular intervals. A piRNA-based host defense was rapidly established in two replicates (R1, R4) but not in a third (R2), whereP-elementcopy numbers kept increasing for over 50 generations. We found that the ping-pong cycle could not be activated in R2 although the ping-pong cycle is fully-functional against other TEs. Furthermore, R2 had both insertions in piRNA clusters and siRNAs, suggesting that neither of them is sufficient to trigger the host defense. Our work shows that control of an invading TE requires activation of ping-pong cycle and that this activation is a stochastic event that may fail in some populations leading to a proliferation of TEs that ultimately threaten the integrity of the host genome.

show abstract

Section: Consequences For Natural Populationsmentioning

confidence: 99%

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Selvaraju,

Wierzbicki,

Kofler

2024

Genome Res.

View full text Add to dashboard Cite

show abstract

Patterns of piRNA regulation inDrosophilarevealed through transposable element clade inference

Said

McGurk

Clark

et al. 2021

Preprint

View full text Add to dashboard Cite

Transposable elements (TEs) are self-replicating "genetic parasites" ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their brethren. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population-specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a co-evolution of TEs and hosts, where new TE variants arise by mutation, then increase in copy number, and the host then responds by producing antisense piRNAs which may be used to silence these emerging variants.

show abstract

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19^thcentury

Scarpa,

Pianezza,

Wierzbicki

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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

show abstract

Tirant stealthily invaded naturalDrosophila melanogasterpopulations during the last century

Cited by 4 publications

References 131 publications

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Patterns of piRNA regulation inDrosophilarevealed through transposable element clade inference

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19^thcentury

Contact Info

Product

Resources

About

Tirant stealthily invaded naturalDrosophila melanogasterpopulations during the last century

Cited by 4 publications

References 131 publications

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Experimentally evolvingDrosophila erectapopulations may fail to establish an effective piRNA-based host defense against invadingP-elements

Patterns of piRNA regulation inDrosophilarevealed through transposable element clade inference

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19thcentury

Contact Info

Product

Resources

About

Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19^thcentury