Genomic approachs to studying plant evolution, function and phylogeny

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The focus of my research program is to discover how land plants are related to each other (plant phylogeny; tree of life), and to use this information, along with newly sequenced plant genomes, to understand the consequences of major plant life-history shifts. The proposed work includes new training opportunities in genomic methods for diverse students, including undergraduate researchers. The major transitions we study include: (i) the loss of photosynthesis in plants that obtain sugars and other nutrients from soil fungi (mycoheterotrophy), instead of using sunlight (photosynthesis), (ii) domestication of 'minor' crops in the Andes, and (iii) the origin of a carnivorous plant which preys on insects for essential elements missing in its boggy habitats. We also infer phylogenies in other groups of interest, including Hydatellaceae. We will explore challenging aspects of phylogenetic inference, including elevation of evolutionary rates in the genomes of non-photosynthetic plants. Genome sequencing technology has advanced enough to sequence plant genomes (chloroplast, mitochondrial and recently the nuclear genome) with relative ease using whole genome sequencing approaches. We will do this for several plants of interest. A major task is to then assemble, annotate and study the genomes with respect to biologically interesting questions, for example to determine if there is expansion or deletion of genes and gene families related to major functional shifts, and to test for changes in natural selection in retained genes. Plant genomes can be compared to relatives to better understand these changes (e.g., crops to their crop wild relatives; carnivorous plants to non-carnivorous relatives). Similar comparative genomic approaches allow us to discover and characterize parallel (convergent) evolution related to the shift (e.g. gene loss and genome reduction related to the loss of photosynthesis). We will also use target-enrichment approaches to pull out large sets of nuclear genes, allowing us to better estimate species phylogenies from gene trees. We will use that approach in several phylogeographic studies, including the Andean tuber crop olluco, and a carnivorous plant, Triantha occidentalis. This approach can be used to include degraded DNAs in the study (e.g., from herbarium specimens). Finally, we will set up an experimental system to better understand the evolutionary loss of photosynthesis. Shading experiments will be done for two partially mycoheterotrophic orchid species, which can grow facultatively without sunlight, by relying on partnerships with various soil fungi. Possible shifts in fungal partners (= root microbiomes) and in the degree of expressed heterotrophy (assessed by quantifying stable isotopes) will also be measured. Plant transcriptomes (the expressed genes in root and shoot tissues) will be sequenced and compared across treatments, and to wild relatives with partial heterotrophy through to full loss of photosynthesis.