Claude dePamphilis

Education

PhD, University of Georgia

Research Interests

Plant Molecular Evolution and Systematics

I am a plant evolutionary biologist with broad interests in processes and patterns of evolution at both the molecular and organismal levels. My research is focused in three areas: (1) the evolution of the flower and the floral developmental program, (2) the study of parasitic plants, and (3) the chloroplast genome and phylogenomic evolution.

Evolutionary Genomics of the Flower

The sudden appearance of flowers in the fossil record over 100 million years ago represents a great mystery that has long puzzled plant and evolutionary biologists. Among the many key questions surrounding the origin and diversification of flowers are: (1) Did the earliest flowers possess the full complement of genetic information needed to assemble a modern flower? (2) Was genome duplication an important driver of the diversification of floral developmental pathways? (3) Are there genes that have conserved functions throughout much of flowering plant history? Recent studies in plant developmental genetics and genomics have identified more than 100 genes with specific roles in flower development in Arabidopsis and other model organisms. Other genes with critical roles may remain undiscovered, largely because of functional redundancy or lethality of loss-of-function mutations. This knowledge, along with the recently clarified phylogenetic relationships of flowering plants (see Leebens-Mack et al. 2005) and the availability of genome-scale data and bioinformatics analysis now make it possible to begin to understand how floral developmental pathways originated and diversified.

The Floral Genome Project (FGP), a multi-institutional, multi-collaborator study funded through the National Science Foundation’s (NSF’s) Plant Genome Research Project, was initiated to address these questions by studying the evolutionary diversification of floral regulatory genes and pathways throughout the major lineages of flowering plants. The study was designed to capture a large number of genes expressed during early flower development in 15 phylogenetically critical lineages of flowering plants and gymnosperms, and to determine their expression patterns at several levels of resolution. We then link the sequences and expression patterns through phylogenetic and molecular evolutionary analysis to infer the gene sets and expression patterns that may have been present in the earliest angiosperm lineages. As the principle investigator of the FGP, my group is involved in many aspects of the project, including library building, screening, and sequencing; studies of individual floral gene families; database construction; and a wide range of bioinformatic and molecular evolutionary studies.

Parasitic Plants

Another long-term focus of our research is the study of parasitic plants, including their phylogeny, biology, and molecular evolution. Although most plants are autotrophic, several thousand species of angiosperms obtain water, minerals, and fixed carbon heterotrophically, using specially modified roots (haustoria) that extract these materials directly from a host plant. In addition to their intrinsic interest as organisms with complex adaptations for direct feeding upon other plants, some parasitic plants are important crop plants and, thus, are of great economic significance. Furthermore, because some parasites have completely lost the ability to photosynthesize, these plants provide a powerful system for the investigation of the effects of drastically altered functional constraints on gene and genome evolution and function.

Chloroplast Genomes

Through a project funded by NSF’s Biocomplexity and Tree of Life programs, we are participating in the first large-scale chloroplast genome sequencing project focused on angiosperms and other seed plants. Our goal is to sequence, annotate, and analyze more than 55 chloroplast genomes that represent all major lineages of flowering plants and gymnosperms, with a special focus on evolutionarily interesting genomes that have undergone rearrangements or gene content changes. Within this larger study, our lab’s focus has been on the chloroplast genome evolution in parasitic plants, monocots, and basal angiosperms.