The gene set defining the diatom chloroplast – BrownCut

Task 1 Defining the BrownCut
Task 2 Expression analysis
Task 3 Functional studies

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Diatoms are a major group of unicellular photosynthetic eukaryotes in aquatic environments. Evolutionarily, these algae are only distantly related to green algae and plants. Whilst these latter organisms are derived from the primary endosymbiosis of a cyanobacterium into a phagotrophic eukaryote, diatoms and related organisms within the stramenopile group of eukaryotes are derived from a secondary endosymbiosis, involving the fusion of at least a red alga and green algae with another eukaryote. Diatoms therefore display distinctive cellular and metabolic features compared to organisms of the green lineage. In the last decades, genomic investigation of different diatom species has started to unveil the chimeric nature of diatom genomes. Pioneering functional characterizations of diatom specific genes have also contributed to identify important diatom metabolic innovations, broadening our appreciation of the diversity of secondary plastid-bearing organisms and of the complex strategies controlling their growth and productivity in aquatic environments. Recent progress in environmental genomics, oceanography and ecology now allow to test for the presence and expression of genes of interest in situ, thereby extending laboratory-based knowledge to natural ecosystems.
However, despite this important progress and the well-recognized ecological role of diatoms for sustaining life on Earth, the mechanisms controlling diatom biology are still largely unknown. Current understanding about the regulation of diatom photosynthesis is still limited and fundamental questions about plastid evolution and activity remain.

In order to fill this important knowledge gap, we propose here to define the BrownCut, the nuclear-encoded chloroplast-targeted proteins that are specific to diatoms, and not found in red or green algae.  This project is inspired by the GreenCut, a bioinformatically-derived inventory of proteins found in the green lineage but absent in non-photosynthetic organisms, generated using the genome of Chlamydomonas. Research on the GreenCut has been transformative for dissecting photosynthesis and its regulation.  

The proposed approaches are based on exploitation of a range of mature resources and that will be brought together specifically for the current work: the GreenCut gene set ; an ancient stramenopile chloroplast proteome, extensive diatom transcriptomics data from the global ocean, and a transformable diatom species, Cyclotella cryptica, that is unique in being able to assess the functions of genes encoding essential components of photosynthesis in diatoms.

To achieve these goals, BrownCut has gathered a consortium of international standing with an undisputed leadership in diatom genomics, evolution, functional genomics, systems ecology and biology (P1, C. Bowler team) and microalgae biology, genomics, genetics (diatoms and Chlamydomonas), photosynthesis, chloroplast biology and evolution (P2, A. Falciatore team). We are confident that the proposed integrative study will contribute to fill the current gap in knowledge between the physiological functions of secondary-plastid-bearing algae and the evolutionary mechanisms that have led to their success and diversification. BrownCut will provide major insights into the processes underpinning photosynthesis in diatoms, indeed essential for understanding the effect of climate change on marine phytoplankton and the ecosystems they sustain.