Flowering plants are important because they underpin much of planetary ecology, priming the food chains that power terrestrial ecosystems, and providing us with most of our material needs (oxygen, food, fuel, pharmaceuticals, etc). The study of a few highly specialized model plants (such as Arabidopsis) has been a particularly powerful paradigm for understanding the functional biology of plants. These studies are currently being integrated with large-scale DNA sequencing studies of diverse plant genomes, allowing plant biologists to unravel patterns of gene diversification (= phylogenetics), and facilitating predictive studies of gene function in a comparative biological framework (= phylogenomics). Functional plant biologists have focused the bulk of their attention on the monocots and eudicots, the two largest groups of flowering plants. Until now we have lacked an early evolving angiosperm to provide a meaningful point of comparison for phylogenomic studies of existing model plant systems, and of the crop plants that underpin much of the European agroeconomy. Trithuria submersa in the family Hydatellaceae is being developed as a new model system to fill this important gap. I propose to develop large-scale phylogenetic data sets from genomic data that have been generated for this family. I will use this to resolve the branching order of the first flowering plants, which include Hydatellaceae. This will address a major conundrum in plant biology that has been unresolved since the time of Charles Darwin. I will also explore how these data sets can be used as a tool to better predict gene function and orthology (relatedness) in other major groups of flowering plants. Finally, I will resolve a key problem in the species biology of Trithuria submersa concerning its genetic boundaries, as it is currently unclear if this plant is a single highly diverse species or up to three distinct but closely related species.