ArticleNucleic acids research2020
Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Transposable elements contribute substantially to naturally occurring genetic lethality in Drosophila melanogaster.PLoS biology · 2026Article
- Rapid evolution and comparative analysis of piRNA clusters inbioRxiv : the preprint server for biology · 2026Article
- Near complete assembly of Drosophila melanogaster Canton S strain genome.Nature communications · 2025Article
- The Role of PIWI-Interacting RNA in Urologic Carcinoma and Its Clinical Implications.Cancer reports (Hoboken, N.J.) · 2025Review
- Spatiotemporal Tracking of Three Novel Transposable Element Invasions in Drosophila melanogaster over the Last 30 Years.Molecular biology and evolution · 2025Article
- Rapid evolution of piRNA clusters in theGenome research · 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
- Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s.PLoS genetics · 2024Article
- The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model.BMC biology · 2023Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain ofInternational journal of molecular sciences · 2022Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Temperature-dependent Small RNA Expression Depends on Wild Genetic Backgrounds of Caenorhabditis briggsae.Molecular biology and evolution · 2022Article
- Ongoing endeavors to detect mobilization of transposable elements.BMB reports · 2022Review
- Sex-specific variation in R-loop formation in Drosophila melanogaster.PLoS genetics · 2022Article
- Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.Nature communications · 2022Article
- Article
- Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference.Molecular biology and evolution · 2022Article
- A review of strategies used to identify transposition events in plant genomes.Frontiers in plant science · 2022Review
- Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis.GigaScience · 2021Article
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2 authors.
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Abstract
Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.
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