TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Eukaryotic genomes are generally rich in repetitive sequences. LTR retrotransposons are the most abundant class of repetitive sequences in plant genomes. They form segments of genomic sequences that accumulate via individual events and bursts of retrotransposition. A limited number of tools exist that can identify fragments of repetitive sequences that likely originate from a longer, originally unfragmented element, using mostly sequence similarity to guide reconstruction of fragmented sequences. Here, we use a slightly different approach based on structural (as opposed to sequence similarity) detection of unfragmented full-length elements, which are then recursively eliminated from the analyzed sequence to repeatedly uncover unfragmented copies hidden underneath more recent insertions. This approach has the potential to detect relatively old and highly fragmented copies. We created a software tool for this kind of analysis called TE-nester and applied it to a number of assembled plant genomes to discover pairs of nested LTR retrotransposons of various age and fragmentation state. TE-nester will allow us to test hypotheses about genome evolution, TE life cycle and insertion history. The software, still under improvement, is available for download from a repository at https://gitlab.fi.muni.cz/lexa/nested.