Genomic re-assessment of the transposable element landscape of the potato genome

Abstract

Transposable elements are DNA sequences with the ability to auto-replicate and move that occupy large proportions of the host genome. TEs are responsible for shaping the genome size and are major drivers of gene regulation, epigenetics, stress regulation and genome evolution. Given their significance, the development of clear and efficient TEs annotation pipelines has become essential for many species. The latest TE discovery de novo-based methods tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform an improved detection, classification and annotation of reliable potato TEs throughout an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Previous TEs annotation for this genome varied from 20 to 34% genome coverage. However, our pipeline revealed that only ca. 16% of the genome can clearly be annotated as TEs. Since we used a variety of tool, approaches and rules, our results suggest that several TEs annotation projects might overestimate annotations. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTRs families which display a distinct pattern between the two major families. Thus, older Gypsy elements concentrated around heterochromatic regions and younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TEs annotation files, but also all the necessary steps to performed de novo detection for other species.