Brown algae (Phaeophyceae), or brown seaweeds, are multicellular macroalgae that belong to the larger eukaryotic Stramenopile supergroup, which also includes microalgae (e.g., diatoms) as well as heterotrophic protists (e.g., oomycetes). Like plants and animals, brown algae are one of the small number of lineages that evolved complex multicellularity. Yet, the evolutionary process leading to multicellularity in brown algae has been quite distinct, leading to the acquisition of some unique characteristics which are absent in the other lineages. This project aims to deepen the understanding of the molecular processes underlying brown algae development and acquisition of multicellularity through an analysis of the functional regulatory roles of long non-coding RNAs (lncRNAs), key actors in cellular regulation across the Eukarya domain of life. It will employ a multidisciplinary approach, for which the three partners involved have demonstrated expertise, involving comparative genomics and trancriptomics, computational biology, functional biology and epigenomics to characterize how lncRNAs control gene expression programs that define distinct development states in brown algae. Ectocarpus sp. and Saccharina sp. will be used as preferred model systems since they show distinct developmental morphologies but are evolutionary close. On a fundamental level, the BrownLincs project will provide new knowledge on brown algal development regulation and acquisition of complex multicellularity. On a more applied level, this project has the potential to provide novel molecular tools to enable the engineering of high biomass production in brown algae that can be explored to produce new generation, added value materials for food, feed and other industrial applications, in a blue economy context.