Stramenopiles (also known as heterokonts) are a major eukaryotic phylum with an amazing diversity of forms and lifestyles. They are most often unicellular, such as diatoms and many heterotrophic flagellates, but also multicellular, like the brown algae. They can be free-living or parasitic, photosynthetic or heterotrophic and are found in all common environments. They have been especially successful in marine habitats as key players in the food web as primary producers (e.g., diatoms) and predators of bacteria. Recently, many new stramenopile lineages have been found among the most abundant species in marine plankton, which have collectively been called MAST (MArine STtramenopiles). Other species are important parasites of animals and plants (e.g., Blastocystis and oomycetes) and represent significant medical and economic threats. However, despite their ecological and societal importance, little is known about the genomics of most contemporary stramenopile lineages and about the early evolution and the characteristics of ancestral stramenopiles that could explain their adaptations and their current huge diversity and ecological success. We will address these questions using two complementary approaches: 1) Sequencing genomes and transcriptomes of 20 species of diverse basal-branching stramenopiles to infer the gene content and genome traits of stramenopile ancestors by comparative genomics and phylogenomics; 2) surveying marine species in the bay of Villefranche at various depths along 2 years with microscopy, flow cytometry, and molecular methods (massive 18S rRNA gene sequencing and metatranscriptomics using the new genome data as a reference), in combination with plankton manipulation experiments to identify biotic (e.g., predation) and abiotic (e.g., temperature) parameters that influence the size and composition of marine stramenopile populations. ANCESSTRAM will produce various types of deliverables, the most important ones including 1) isolation of new MAST species; 2) complete genome and transcriptome sequences of 20 stramenopiles (new isolates and culture collection species); 3) characterization of the diversity and dynamics of stramenopile populations in surface and aphotic regions of the bay of Villefranche-sur-Mer during a complete 2-years survey; 4) whole community mRNA sequences (metatranscriptomes) of surface and deep plankton samples of Villefranche and identification of stramenopile genes expressed at different depths; 5) qualitative and quantitative data on the occurrence of stramenopiles and the composition of the microbial plankton community in Villefranche; 6) a highly resolved stramenopile phylogeny based on hundreds of conserved markers; 7) identification of the gene content in ancestral nodes of the stramenopile phylogeny, including the ancestors of key groups (e.g., the photosynthetic clades or the parasitic Blastocystis and oomycetes clades); and 8) identification of genes acquired by horizontal gene transfer from different donors (e.g., bacteria) that may have been involved in relevant specific adaptations (such as plant and animal parasitism or photosynthesis). We will thus produce significant new knowledge on these very diverse and ecologically important organisms and will help to better understand the evolutionary history of stramenopile groups that impact human activities, including human (Blastocystis) and plant (oomycetes) parasites, and the origin of the genes that differentiate them from free-living species, which may become interesting applied targets to fight them more efficiently. The new genome and transcriptome sequences will reveal clues to explain the extraordinary phenotypic plasticity of this group and its wide spectrum of forms and lifestyles. Finally, the ecological and metatranscriptomic studies will serve to identify the set of genes expressed under different environmental constraints and give clues to understand their remarkable ecological success in marine environments.