ArticlePLoS genetics2012
Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
129 citing papers in PubMed, 280 citations in OpenAlex.
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Influence of geography, seasonality and experimental selection on Chironomus riparius recombination rates.BMC genomics · 2026Article
- Meiotic double-strand DNA breaks and spontaneous mutation in Drosophila melanogaster.G3 (Bethesda, Md.) · 2026Article
- Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.Genome biology and evolution · 2026Article
- Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen.Nature communications · 2025Article
- Purifying selection shapes the dynamics of P-element invasion in Drosophila simulans populations.Genome biology · 2025Article
- Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome.Nucleic acids research · 2025Article
- Tolerance thresholds underlie responses to DNA damage during germline development.Genes & development · 2024Article
- Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.Genome biology and evolution · 2024Article
- Experimental evolution of hybrid populations to identify Dobzhansky-Muller incompatibility loci.Ecology and evolution · 2024Article
- The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model.BMC biology · 2023Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- Transposable elements drive the evolution of metazoan zinc finger genes.Genome research · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Genetic differentiation following recent domestication events: A study of farmed Nile tilapia (Evolutionary applications · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- The Transposition Rate Has Little Influence on the Plateauing Level of the P-element.Molecular biology and evolution · 2022Article
- Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.Plant communications · 2022Article
- Epistatic selection on a selfisheLife · 2022Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Transposable elements (TEs) are mobile genetic elements that parasitize genomes by semi-autonomously increasing their own copy number within the host genome. While TEs are important for genome evolution, appropriate methods for performing unbiased genome-wide surveys of TE variation in natural populations have been lacking. Here, we describe a novel and cost-effective approach for estimating population frequencies of TE insertions using paired-end Illumina reads from a pooled population sample. Importantly, the method treats insertions present in and absent from the reference genome identically, allowing unbiased TE population frequency estimates. We apply this method to data from a natural Drosophila melanogaster population from Portugal. Consistent with previous reports, we show that low recombining genomic regions harbor more TE insertions and maintain insertions at higher frequencies than do high recombining regions. We conservatively estimate that there are almost twice as many "novel" TE insertion sites as sites known from the reference sequence in our population sample (6,824 novel versus 3,639 reference sites, with on average a 31-fold coverage per insertion site). Different families of transposable elements show large differences in their insertion densities and population frequencies. Our analyses suggest that the history of TE activity significantly contributes to this pattern, with recently active families segregating at lower frequencies than those active in the more distant past. Finally, using our high-resolution TE abundance measurements, we identified 13 candidate positively selected TE insertions based on their high population frequencies and on low Tajima's D values in their neighborhoods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.