Comparative genomic and phylogenetic approaches for investigating plant diversity and evolution

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The focus of my research program is to discover how land plants are related to each other, and to use this information to understand major life-history shifts across the plant tree of life. The first component of our proposed work uses genome-focused approaches to reconstruct phylogenetic relationships for a broad range of plant groups. We will apply this knowledge to understand what happens in plant lineages that have lost the ability to photosynthesize (the process by which plants use energy from the sun to produce glucose from carbon dioxide and water). The non-photosynthetic plants of interest, called mycoheterotrophs, have evolved convergently around 50 times in different plant groups. They rely on soil fungal partners for their fixed carbon and other nutrients. We propose to examine how all three plant genomes of mycoheterotrophs are affected by this major nutritional shift. We will perform detailed studies of the two organellar genomes found in plant cells, the plastid and mitochondrion. The plastid genome is expected to be especially prone to modification and degradation in response to the evolution of obligate heterotrophy, as the plastid’s primary role (as the chloroplast of green plants) is to perform photosynthesis. We will test and refine models for how this genome degrades following the loss of photosynthesis, by sequencing plastid genomes from multiple mycoheterotrophic plant groups, allowing us to screen for convergent patterns of gene loss and retention. The effect of photosynthesis loss on the plant mitochondrial genome is much less well understand, and will also be addressed by looking for convergent patterns of change in this organellar genome. We will also use focused transcriptome studies of the nuclear genome to look at shifts in gene expression in nuclear-encoded organellar genes. Finally, we will employ tests to detect instances of relaxed selection in lineages undergoing major life-history shifts, such as the origin of mycoheterotrophy. For example, the timing of shifts in selection intensity may predate a noticeable life-history change, if the environment is already acting on subsets of genes prior to the major shift. We will address this by looking at the effects of multiple types of life-history shifts, including mycoheterotrophy, in addition to convergent losses of a major plastid protein complex (NAD(P)H dehydrogenase) in submerged aquatic plants (land plants that returned to the water) and carnivorous plants. The proposed work includes new training opportunities in genomic methods for students, including undergraduate researchers.