RSRCH Research Computing
Office of VP for Research
Office of VP for Research
Fungal and Plant Symbioses: Genetics, Genomics, and Epigenetics
The McDonald lab investigates aspects of fungal and plant genetics with an emphasis on symbiotic interactions. Projects include:
- Sequencing and assembling the genomes of lichenizing fungi and their symbiotic green algae and cyanobacteria: One-fifth of all described species of fungi form obligate and persistent symbiotic relationships with green algae and/or cyanobacteria as their sole means of obtaining the carbon needed to sustain their lives. These symbioses are called lichens, and the fungi that participate in them are known as lichenizing fungi. These fungi are understudied for many reasons, including that their obligate symbiotic nature and slow rate of growth make them difficult to culture in the lab. Consequently, the genomes of lichenizing fungi are vastly underrepresented compared to the genomes of other fungi. The McDonald lab aposymbiotically cultures lichenizing fungi from five taxonomic classes of fungi and sequences their genomes. These genome sequences pave the way for downstream analyses of RNA-seq data from both the various structures that compose the lichenized thalli and the aposymbiotic symbionts to determine which genes are involved in the various stages of symbiotic development.
- Horizontal gene transfer in the phylogeny of ammonium transporters: Proteins in the AMT/MEP/Rh family facilitate the movement of ammonia or ammonium across the cell membrane. To date at least three mechanisms of transport have been described for proteins in in this protein family. Some of the proteins are gas channels conducting ammonia gas (NH3), others are modified gas channels that deprotonate ammonium (NH4+), conduct ammonia through the pore, and reprotonate the molecule again on the cytoplasmic side, while still others are bone fide ammonium transporters that conduct ammonium across the membrane. Ammonium transport sensu stricto has been described only from monocot and dicot plants. The McDonald lab clones putative ammonium transporters from additional lineages of land plants, green algae, and other groups of organisms to identify the evolutionary origin of ammonium transport. Electrophysiology of select transporters is performed in collaboration with the lab of Professor John Ward (Plant Biology).
- Identification of fungal virulence factors from pathogenic fungi: Cryptococcus neoformans is a facultative pathogen of humans. Although this basidiomycete yeast is easily combatted by a healthy human immune system, people with compromised immune systems are subject to infection. The infection begins in the lungs, then the fungus disperses into the blood stream and ultimately crosses the blood-brain barrier, causing meningitis which is often fatal. In sub-Saharan Africa, cryptococcal meningitis is the second most common infection due to HIV/AIDS, and is the fourth leading cause of death from infectious disease in this region. The population structure of this fungal pathogen varies from site to site: in Uganda, the population is dominated by one highly pathogenic strain of the fungus, whereas in South Africa, many more strains of the fungus are present in the patient population and no one strain predominates. In collaboration with the lab of Professor Kirsten Nielsen (Microbiology and Immunology) the McDonald lab performs multi-locus sequence typing (MLST) and uses Illumina sequencing to genotype fungal isolates from patient cerebral spinal fluid (CSF) in 3 locations in sub-Saharan Africa as part of a larger collaboration between the University of Minnesota and universities and hospitals in Kampala, Uganda; Mbarara, Uganda; and Cape Town, South Africa.
Dr. Tami McDonald