Regulatory sequence evolution during major transitions in complex multicellularity in the brown algal radiation

Brown algae are a multicellular clade that display remarkable diversity in developmental and physiological complexity, and in life history traits.

They evolved independently and more recently than animals and plants, making them a uniquely powerful system to characterise the genomic changes that underlie the emergence of complex multicellularity.

I will specifically test the hypothesis that cis-regulatory element (CRE) evolution plays a leading role the evolution of complexity.

Harnessing large-scale multiomics datasets, I will quantify lineage-specific rates of CRE gains and losses, and attempt to link these events to transitions in complexity.

I will combine signatures of constraint from a 59-species whole-genome alignment with functional epigenomic data (ATAC-seq, ChIP-seq) from five representative species to produce fine-scale maps of deeply conserved and recently acquired CREs.

To understand the mechanisms of CRE evolution, I will annotate transposable elements (TEs) and quantify variation in TE diversity, abundance and activity. I will characterise what roles TEs have had in CRE dissemination. I will also explore between-species variation in the proportion of proximal and distal CREs.

I will analyse high-resolution Hi-C data for four species to ask what effect distal regulation has on 3D genome organisation (i.e. are distal CREs and the genes they regulate topologically associated?).

PhaeoCREEvol will inform upon the rates and mechanisms of CRE evolution during the emergence of complexity, providing a highly pertinent comparison to animals and plants.

This will increase our knowledge of regulatory evolution in general, while shedding light onto the fundamental biology of a largely unstudied eukaryotic group.

Brown algae play critical ecological roles and have significant potential to mitigate climate change, enhance global food security, and deliver novel industrial solutions, providing key motivations to better understand their genetics and evolution.