GenomeDelta: detecting recent transposable element invasions without repeat library.

Autor: Pianezza R; Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.; Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria., Haider A; Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria., Kofler R; Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria. rokofler@gmail.com.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2024 Dec 18; Vol. 25 (1), pp. 315. Date of Electronic Publication: 2024 Dec 18.
DOI: 10.1186/s13059-024-03459-5
Abstrakt: 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.
Competing Interests: Declarations. Ethics approval and consent to participate: Ethics approval is not applicable for this study. Competing interests: The authors declare no competing interests. Robert Kofler was a Guest Editor for this article collection but was not involved in the editorial process of this manuscript.
(© 2024. The Author(s).)
Databáze: MEDLINE
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