ArticleNucleic acids research2015
Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- Male sterility in Drosophila hybrids revealed by a multi-generational transcriptomic analysis of genes and transposable elements in testes.BMC biology · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility.Nucleic acids research · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- A unified framework to analyze transposable element insertion polymorphisms using graph genomes.Nature communications · 2024Article
- Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes.Mobile DNA · 2024Article
- Tolerance thresholds underlie responses to DNA damage during germline development.Genes & development · 2024Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
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- High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin.Genetics · 2023Article
- The highly improved genome ofLife science alliance · 2023Article
- ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.Nucleic acids research · 2023Article
- Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster.Nucleic acids research · 2023Article
- Effects of Wolbachia on Transposable Element Expression Vary Between Drosophila melanogaster Host Genotypes.Genome biology and evolution · 2023Article
- Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism.BMC biology · 2022Article
- High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation.Nature communications · 2022Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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Abstract
To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.
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