ArticleNature communications2022
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- Updated Transposable Element Libraries forbioRxiv : the preprint server for biology · 2026Article
- The ongoing invasion of the endogenous retrovirus Kuruka in natural Drosophila melanogaster populations.Nature communications · 2026Article
- Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse.bioRxiv : the preprint server for biology · 2026Article
- Evidence for dual pathways of Tc1/mariner domestication in Drosophila.BMC biology · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore.G3 (Bethesda, Md.) · 2026Article
- Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding.Nature genetics · 2026Article
- Meiotic double-strand DNA breaks and spontaneous mutation in Drosophila melanogaster.G3 (Bethesda, Md.) · 2026Article
- Transgenerational effects of heat shock on gene regulation and fitness-related traits in natural Drosophila populations.Molecular biology and evolution · 2026Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Beyond inversions and deletions: the evolutionary and functional insights from translocations, fissions, and fusions in animal genomes.Heredity · 2026Review
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Polymorphic 3D genome architecture mediated by transposable elements.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD.Genetics · 2026Article
- Diverging transposon activity among polar bear sub-populations inhabiting different climate zones.Mobile DNA · 2025Article
- Recurrent expansion and rapid evolution of the Drosophilid RNAi pathway in testis.bioRxiv : the preprint server for biology · 2025Article
- Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen.Nature communications · 2025Article
- A comparative analysis of transposable element diversity and evolution across 75 bee genomes.BMC genomics · 2025Article
19 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.
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