Comparative and functional genomics of non-photosynthetic plants

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Some plants steal nutrients and/or water from regular green plants and consequently have reduced or completely lost their ability to photosynthesize. We study plastid genomes (plastomes) in a variety of these so-called heterotrophic plants (commonly known as parasitic plants), with the goal of answering the central question: can the plastome be lost entirely or is it essential that particular genes be retained in this genome? Comparative analyses of the plastomes along the full trophic spectrum, from autotrophy to mixotrophy to full heterotrophy, will allow us to assess the degree to which genomic changes take place prior to complete loss of photosynthesis, and to dissect the evolutionary pressures on plastomes exerted by other plastid metabolic functions. Many groups of heterotrophic plants arose separately from their respective photosynthetic relatives. The basic idea we take advantage of in this proposal is that each of those lineages of heterotrophs represents an independent natural genetic experiment whose plastomes and other genomes have (co)evolved under relaxed functional constraints. Each lineage has adopted a unique suite of expressed genes and therefore represents one solution to "deconstructing" complex nuclear-organellar metabolic pathways. Given the difficulties or even the impossibility of reverse genetic approach in this system, a study that replicates over multiple natural plastid “mutants” will contribute to our deeper mechanistic understanding of photosynthesis, its molecular components, and their interaction. We will conduct an extensive study of organellar genome content, sequence, and expression patterns in heterotrophic plants and their closest autotrophic relatives in order to ultimately be able to integrate genomic, functional, and evolutionary data. This will be achieved by sequencing transcriptomes and/or whole genomes in a large number of heterotrophic plants, comparison of results found in evolutionarily distinct groups, and doing so in a well established historical context. These new next-generation sequencing data will allow us to test the predictions that some genomic changes precede the evolution of full-blown heterotrophy, that there are limits to how reduced plastomes can be, as well as to ascertain whether the patterns of plastome evolution are gradual or stepwise (punctuated). This investigation will complement other studies being performed in closely related areas and will impact the fields of biotechnology, genomics, molecular evolution, physiology, synthetic biology, and systematics.