Epigenetics and the Evolution of Plant Genomes
Transposable elements (TEs) comprise the majority of angiosperm genomic DNA, and their presence is counteracted by methylation. Methylation affects not only the activity of transposable elements but also the function of nearby genes. But TEs are not the only component of the genome that is methylated; so are genes. We are taking an evolutionary approach to study many aspects of methylation and other epigenetic features – i.e., Why are genes methylated? When did methylation evolve? Are TEs controlled targeted differentially for silencing by small RNAs (siRNAs)? How does methylation variation contribute to genome size differentiation and ultimately interspecific divergence?
E.Coli Experimental Evolution
With collaborators at UCI, we have evolved 120 lines of E. coli under high temperature (42 C). We are currently investigating the genetic and mechanistic underpinnings of adaptation to this stressful environment. A key feature of our experiment is its size; the number of evolved lines is an order of magnitude higher than previous experiments. As a result we can ask questions about parallel pathways to adaptation and the number of genetic solutions to the high temperature challenge.
The Genetics of Domestication
Domestication has also been a long-running interest of the lab. Although most work has focused on the population genetics of maize domestication, the lab has also contributed to studies in rice, pearl millet and soybean.
Comparative Genomics & Molecular Evolution
The lab has long been interested in comparisons within and between genomes to characterize evolutionary processes. A primary goal has been to isolate the factors that contribute to evolutionary rates among genes, including gene expression, methylation and psuedogenization. Previous work in comparative genomics has included study of grass species and members of the Brassicaceae, as well as pox and herpes viruses.