Post-Transcriptional Gene Regulation in Fungi
Gene regulation occurs at many levels in the cell. Understanding the players and role of transcriptional and post-transcriptional regulation controlling development in fungi will provide insight into the evolution of development. We are exploring the role of smallRNAs in fungi and how they play a role in regulation of gene expression controlling development. This work is performed in the filamentous fungus Neurospora crassa applying genetic and genomic tools.
Gene family and genome evolution
What role does duplication play in genome evolution? Gene families change in size in different lineages. We are interested in quantifying how much change is due to neutral evolution and what kinds of gene family size changes are driven by direction selection. How does this duplication compare to the proliferation and control of transposons and retroviral elements in fungal genomes? In some fungi including N. crassa there are pathways limiting duplication including Repeat Induced Point mutations (RIP) and silencing of unpaired DNA (MSUD). How do gene families evolve and duplications fix in these fungal lineages and what strategies for replication have succeeded for some transposon families?
Evolution of fungal cell wall
The cell wall protects and partitions the cell’s internal components from the outside world, but is permeable allowing materials and chemical signals to be transported. The composition of the cell wall varies across the fungal kingdom from the aquatic chytrids to the zygomycetes, and ascomycete and basidiomycete fungi. We seek to describe the differences in cell walls comparing lineages of early branching fungi and understand the evolution of the genes that synthesize and assemble the cell wall components. We will use enzymatic and imaging approaches to visualize and quantify cell wall composition in a variety of fungi and connect this to genome composition of cell wall biosynthesis, remodeling, and related genes via genome sequencing and comparative genomics. This work extends from our work on the early diverging chytrid fungi like Batrachochytrium dendrobatidis.
Methods for comparative and population genomics
Genome sequencing so affordable and accessible that nearly any fungal genome can be sequenced. Managing the data from the currently over 100 fungal genomes and integrating new data requires disciplined software and data management approaches. We build tools to mining these data to address research questions from phylogenetics and systematics, molecular evolution and population genetics, to predicting metabolic and enzymatic capabilities.
A summary of some of the work that interests can be seen in recent presentations archived here or via news posts.
