Characterization of the transposable element landscape shaping the Ectocarpus genome

Abstract

Comprising up to 90% of eukaryotic genomes, transposable elements (TEs) are mobile genetic units that play fundamental roles in evolution. Brown algae, one of the most complex multicellular eukaryotic groups that evolved independently from plants, fungi, and animals, are particularly underexplored in their transposon biology, especially when studied in a developmental context. Here, we explore the TE landscape of the model brown alga Ectocarpus, using a high-quality genome assembly complemented by extensive manual curation. TEs account for 28% of the genome, with a predominance of evolutionarily young elements. DNA transposons represent the most abundant and diverse TE subclass. Notably, TEs are significantly enriched along the sex chromosomes, a pattern potentially driven by local transposition events from the non-recombining sex-determining region into the pseudoautosomal regions. The genome harbors a high density of intronic TEs, which show minimal impact on host gene expression; however, intronic TEs tend to be shorter and more degraded than intergenic copies, suggesting selective pressures on their retention in the genome. Intact and potentially active TEs are preferentially associated with small RNAs and the histone modification H3K79me2, with over 70% of H3K79me2-marked intact TEs also enriched in small RNAs. This stable association indicates tight and sustained silencing of intact TEs throughout the life cycle of Ectocarpus. Our study highlights the genetic diversity of the Ectocarpus mobilome and presents a complex, multilayered landscape of TE regulation mechanisms which involves small RNAs and chromatin modifications in the absence of an epigenetic silencing machinery that would be comparable to animals or plants.