GenomeDelta: detecting recent transposable element invasions without repeat library
Abstract We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is ap...
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| Format: | Article |
| Language: | English |
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BMC
2024-12-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03459-5 |
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| author | Riccardo Pianezza Anna Haider Robert Kofler |
| author_facet | Riccardo Pianezza Anna Haider Robert Kofler |
| author_sort | Riccardo Pianezza |
| collection | DOAJ |
| description | Abstract We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici. |
| format | Article |
| id | doaj-art-e2817039e5b6462db6a8f66227ee69e6 |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-e2817039e5b6462db6a8f66227ee69e62025-01-26T12:36:05ZengBMCGenome Biology1474-760X2024-12-0125111610.1186/s13059-024-03459-5GenomeDelta: detecting recent transposable element invasions without repeat libraryRiccardo Pianezza0Anna Haider1Robert Kofler2Institut für Populationsgenetik, Vetmeduni ViennaInstitut für Populationsgenetik, Vetmeduni ViennaInstitut für Populationsgenetik, Vetmeduni ViennaAbstract We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.https://doi.org/10.1186/s13059-024-03459-5Transposable elementsRepeat libraryHorizontal gene transferLateral gene transferNon-model organismsGenome assemblies |
| spellingShingle | Riccardo Pianezza Anna Haider Robert Kofler GenomeDelta: detecting recent transposable element invasions without repeat library Genome Biology Transposable elements Repeat library Horizontal gene transfer Lateral gene transfer Non-model organisms Genome assemblies |
| title | GenomeDelta: detecting recent transposable element invasions without repeat library |
| title_full | GenomeDelta: detecting recent transposable element invasions without repeat library |
| title_fullStr | GenomeDelta: detecting recent transposable element invasions without repeat library |
| title_full_unstemmed | GenomeDelta: detecting recent transposable element invasions without repeat library |
| title_short | GenomeDelta: detecting recent transposable element invasions without repeat library |
| title_sort | genomedelta detecting recent transposable element invasions without repeat library |
| topic | Transposable elements Repeat library Horizontal gene transfer Lateral gene transfer Non-model organisms Genome assemblies |
| url | https://doi.org/10.1186/s13059-024-03459-5 |
| work_keys_str_mv | AT riccardopianezza genomedeltadetectingrecenttransposableelementinvasionswithoutrepeatlibrary AT annahaider genomedeltadetectingrecenttransposableelementinvasionswithoutrepeatlibrary AT robertkofler genomedeltadetectingrecenttransposableelementinvasionswithoutrepeatlibrary |