Systematic annotation of Helitron-like elements in eukaryote genomes using HELIANO

Helitron-like elements (HLEs) are widespread eukaryotic DNA transposons employing a rolling-circle transposition mechanism. Despite their prevalence in fungi, animals, and plant genomes, identifying Helitrons remains challenging. We introduce HELIANO, a software for annotating and classifying autonomous and non-autonomous Helitron and Helentron sequences from whole genomes. HELIANO outperforms existing tools in speed and accuracy, demonstrated through benchmarking and its application to complex genomes (Xenopus tropicalis, Xenopus laevis, Oryza sativa), revealing numerous newly identified Helitrons and Helentrons. In a comprehensive analysis of 404 eukaryote genomes, we found HLEs widely distributed across phyla, with exceptions in specific taxa. Helentrons were identified in numerous land plant species, and 20 protein domains were discovered integrated within specific autonomous HLE families. A global phylogenetic analysis confirmed the classification into main clades Helentron and Helitron, revealing nine subgroups, some enriched in particular taxa. The future use of HELIANO will contribute to the global analysis of TEs across genomes and enhance our understanding of this transposon superfamily.