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

ZAVALLO, DIEGO; CRESCENTE, JUAN MANUEL; GANTUZ, MAGDALENA; LEONE, MELISA; VANZETTI, LEONARDO SEBASTIAN; MASUELLI, RICARDO WILLIAMS; ASURMENDI, SEBASTIAN

PLANT CELL REPORTS

SPRINGER

Lugar: Berlin; Año: 2020

0721-7714

Key message We provide a comprehensive and reliable potato TE landscape, based on a wide variety of identificationtools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.Abstract Transposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the hostgenome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clearand efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, alongwith available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification andannotation through an open-source and freely available pipeline (https ://githu b.com/Diego Zaval lo/TE_Disco very). Using avariety of tools, approaches and rules, we were able to provide a clearly annotated of characterized TEs landscape. Additionally,we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clearclustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertionage and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies.While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantlyon euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all thenecessary steps to perform de novo detection for other species.