Long terminal repeat retrotransposons (LTR-RTs) significantly contribute to the genomic composition and evolution of higher plants, comprising up to 75% of their nuclear DNA. These elements have roles that range from causing genomic disruption to facilitating adaptive changes. Traditional methods for the identification and annotation of LTR-RTs have primarily relied on structure-based approaches, focusing on LTR sequences and generally limiting classification to the Ty3/gypsy and Ty1/copia superfamilies. However, these methods face challenges in genomes with high levels of tandem repeats or nested LTR-RT insertions, and often result in a significant number of false positives.
To improve upon these limitations, we introduce DANTE, a computational pipeline for Domain-based Annotation of Transposable Elements that performs classification of the elements into phylogenetic lineages based on sequences of their conserved protein domains. The identified protein domains are then used by the DANTE_LTR pipeline to annotate complete element sequences by searching for their structural features, such as long terminal repeats, in the adjacent genome regions. As a reference protein database, DANTE and DANTE_LTR use the REXdb database, which contains over 75,000 conserved protein domains from all types of transposable elements found in plants. This protein domain-centered approach enables the subsequent identification of LTR-RT structural features with greater accuracy and a reduction in false discoveries. Moreover, the approach allows for the classification of elements at a more detailed lineage level rather than limiting to broad superfamilies, providing deeper insights into their diversity and evolutionary history.
The DANTE and DANTE_LTR tools are available in command-line versions and also from the Galaxy interface on our RepeatExplorer server (https://repeatexplorer-elixir.cerit-sc.cz/).

References:

Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mobile DNA 10:1.