Shaping Brown Algal Genomes: Evolution and Regulation of Transposable Elements

Abstract

Transposable elements (TEs) are pervasive components of eukaryotic genomes and major drivers of genome evolution, yet they remain poorly characterized in many lineages. Brown algae represent one of the most complex multicellular lineages on Earth and evolved independently from animals, plants, and fungi for over a billion years, but the diversity, distribution, and functional impact of their TEs are still largely unexplored.

This thesis investigates the diversity, genomic distribution, and regulation of transposable elements in brown algae, with a particular focus on the model species Ectocarpus. By generating a comprehensive and curated TE annotation, it establishes a robust resource for comparative analyses across brown algal genomes. Genome-wide analyses reveal that TE composition and distribution vary with genome size and contribute to large-scale genome organization, including a marked enrichment on the sex chromosome driven by specific TE superfamilies. In addition, this study explores TE regulation in a lineage that lacks canonical TE silencing pathways. Integrating small RNA and chromatin profiling data, the results support a multilayered regulatory system involving small RNAs and histone modifications, highlighting alternative strategies for TE control in eukaryotes.

Based on findings consolidated from three studies, this work provides new insights into TE dynamics in brown algae and establishes a framework for understanding their contribution to genome organization, stability, and evolution. More broadly, it expands our perspective on TE regulation across the eukaryotic tree of life by documenting a distinct regulatory landscape in a non-canonical model system.