ArticleJournal of molecular evolution2003
Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes.
Article in Journal of molecular evolution, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 93 citations in OpenAlex.
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Characterization of the transposable element landscape shaping the Ectocarpus genome.Genome biology · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems.The New phytologist · 2025Article
- The genome of the simultaneously hermaphroditic snail Lymnaea stagnalis reveals an evolutionary expansion of FMRFamide-like receptors.Scientific reports · 2024Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
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- The highly improved genome ofLife science alliance · 2023Article
- An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes.Mobile DNA · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Population genomics reveals historical and ongoing recombination in theStudies in mycology · 2021Article
- Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential.BMC genomics · 2021Article
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- Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode.Scientific data · 2020Article
- Population Genome Sequencing of the Scab Fungal SpeciesG3 (Bethesda, Md.) · 2019Article
- RepetDB: a unified resource for transposable element references.Mobile DNA · 2019Article
- Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.PloS one · 2018Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call "TBLASTX strategy," searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, "repeat-based strategy," searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the "TBLASTX strategy" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The "repeat-based strategy" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.
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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.