How complex multicellularity evolves is a fundamental question in biology. The two most complex multicellular groups, animals and plants, each share many core development genes with their unicellular relatives. Thus, it has been hypothesised that increases in gene regulatory sequences, rather than the acquisition of novel genes, may play a central role in the evolution of complexity. However, the ancient origins of developmental complexity in animals and plants has made it difficult to reconstruct the evolutionary steps involved.
Brown algae represent the third most complex lineage on Earth and are vastly understudied relative to animals and plants. They evolved only ~250 million years ago, making them one of the youngest groups with complex multicellularity. Furthermore, extant brown algae exhibit extensive diversity in their complexity, ranging from relatively simple branched filaments (e.g. Ectocarpus) to complex three-dimensional thalli (e.g. kelps). Similar diversity exists in life cycles, sexual systems and genome sizes. Critically, there have been several independent transitions in complexity in the group. Taken together, the recent emergence and diversity of brown algae presents an elegant natural experiment in which to ask what genetic changes coincide with, and have potentially driven, transitions in complexity.
PhaeoCREEvol set out to answer this fundamental question. The project aimed to do this using two key methods. First, it would utilise comparative genomics analyses across the diversity of brown algae (~50 available genomes) to identify conserved noncoding sequences that likely have regulatory function (also known as cis-regulatory elements, or CREs). Second, it would employ multiomics approaches such as ATAC-seq to functionally identify CREs in five species of varying complexity. Combining these data, we would ask whether transitions to greater developmental complexity are associated with lineage-specific increases in CREs. We also aimed to ask how these CREs are acquired, specifically looking at the role of transposable elements, mobile genetic elements that are known to drive CRE evolution in animals and plants. Finally, we set out to ask whether distal gene regulation had emerged in the most complex brown algae using HiC data, mirroring the evolution of long-range gene enhancers in vertebrates and some angiosperms.
The projects main ambitions were to provide fundamental insights in evolutionary biology. Additionally, brown algae are of substantial ecological and economic significance, with brown algal forests forming keystone habitats across 25% of coastlines globally. PhaeoCREEVol also aimed to increase our understanding of brown algal genomics and genetics, bringing benefits to global biodiversity and food security.
