smallRNA sequencing of Ectocarpus male gametophyes and male gametes

Comprising up to 80% of eukaryotic genomes, transposable elements (TEs) are mobile genetic units shaping genome plasticity. The degree of this genomic impact varies broadly across species, which makes each genome unique in its transposon landscape. 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 in the genome of Ectocarpus, a model organism for studying brown algae. We annotated the Ectocarpus mobilome using a high-quality genome assembly which was complemented by a manual curation procedure. TEs account for 28% of the Ectocarpus genome, with a high proportion of evolutionarily young elements, and DNA transposons as the most abundant and diverse subclass. TEs are significantly enriched across the length of the sex chromosomes, which may be driven by local hopping of DNA transposons from the non-recombining sex determining region to the pseudoautosomal regions. The genome harbors a high density of intronic TEs, which appear to have minimal impact on host gene expression. Nonetheless, intronic TEs are shorter and more degraded than intergenic TEs, reflecting potential selective pressures shaping their genomic presence. Through small RNA sequencing and ChIP-seq, we demonstrate that sRNAs and the histone mark H3K79me2 may regulate potentially active TEs across developmental stages. Our findings highlight the complex interplay between TEs and the Ectocarpus genome during development, providing insights into their potential roles during brown algae life cycles.