GenomeDelta: detecting recent transposable element invasions without repeat library

Publikationen als Autor:in / Herausgeber:in der Vetmeduni

Haider, Anna; Pianezza, Riccardo; Kofler, Robert

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.

Dokumententyp

Originalarbeit

Open Access Type

Gold

DOI

10.1186/s13059-024-03459-5

PubMed ID

MEDLINE:39696539

Projekt

Das Verhalten von springenden Genen; Does the size of piRNA clusters predict the abundance of transposable element insertions?