Date on Master's Thesis/Doctoral Dissertation


Document Type

Doctoral Dissertation

Degree Name

Ph. D.



Degree Program

Biology, PhD

Committee Chair

Perlin Michael

Committee Co-Chair (if applicable)

Schultz, David

Committee Member

Schultz, David

Committee Member

Palmer, Kenneth

Committee Member

Running, Mark

Committee Member

Kalbfleisch, Ted

Author's Keywords

Microbotryum violaceum; Smut fungi; RNA-Seq; Agrobacterium-mediated transformation; Genome sequencing; Floral staging


This study made use of the Silene latifolia/Microbotryum lychnidis-dioicae phytopathogen system as the focal system to establish the first reference genome for Microbotryum violaceum sensu lato. In silico analysis was performed on the genome assembly to identify various characteristics of the genome. Using RNA-Sequencing technologies on the Illumina platform, we collected transcriptomic data for both in vitro and in planta life stages of the fungus, providing the most comprehensive look at the gene expression and regulation of this fungus. Due to a lack of identifiable domains on the predicted genes, gene set enrichment analysis was done in context, by including gene sets like “secreted proteins”, “small secreted proteins” and “unique proteins”, to aid discovery of the features in the different datasets. To further research into Microbotryum species in general, we developed, for the first time, a robust and repeatable Agrobacterium-mediated transformation system. Using genomic and transcriptomic data, we were able to select native promoters that drive transcription in specific conditions, making it a highly versatile and controllable system.