Phylogenomics in the Asteraceae

NSF: Project summary


The Compositae (Asteraceae) are a large (25,000-33,000 species) and important family of plants that include critical members of threatened ecosystems and invasives. The most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has unresolved areas. We have developed the tools necessary to enable the rapid sequencing of large numbers of orthologous genes in order to facilitate efficient phylogenomic analyses and the testing of hypotheses of phenotypic evolution across the family.

We have developed a set of sequence capture probes that represent conserved orthologous sequences from existing sunflower, lettuce, and safflower genomic resources. The goal here is to enable the rapid sequencing of large numbers of orthologous genes from a variety of taxa from across the family, thereby facilitating efficient phylogenomic analyses and, ultimately, the testing of hypotheses regarding species relationships and patterns of phenotypic evolution across the family.

Research Partners: The Smithsonian Institute, Oklahoma State University, and University of Arizona

Plant population genetics and genomics

We use population genetic and genomic approaches and tools to ask a variety of questions in our lab. In rare or endangered species, we are interested in the effects of rarity and habitat loss on standing levels of genetic diversity in plant populations. We are interested in the effects of mating system and life history on the spatial structure and genetic diversity. In our lab, we also develop population genetic tools for investigating patterns of clonal genetic diversity. Through genome sequencing and evolutionary genetic analyses, we ask questions about genome conflict and the consequences of organellar heteroplasmy and Non-Mendelian inheritance.

Transgene risk escape via pollen flow in carrot

USDA-NIFA, Project summary

Gene flow between genetically modified crops and their wild relatives has the potential to enhance weediness and/or invasiveness of wild species. In the United States, invasive species have major negative impacts on natural ecosystems, leading to billions of dollars per year in economic and environmental damages, and invasive species are often responsible for the displacement and/or extirpation of native species. We study the potential for gene flow between cultivated carrot and its wild, weedy (admittedly pretty) progenitor, Queen Anne’s Lace using a variety of genetic, genomics, and greenhouse studies. We also investigate heteroplasmy of both the mitochondrial and plastid genomes. #Iheartheteroplasmy

Research Partners: Vanderbilt University

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