Graduate Program

Biological Sciences

Degree Name

Master of Science (MS)

Semester of Degree Completion

2018

Thesis Director

Thomas Canam

Thesis Committee Member

Yordan S. Yordanov

Thesis Committee Member

Gordon C. Tucker

Abstract

This thesis research explored the transcriptional response of Trametes versicolor, a white-rot fungus, in response to fundamentally different types of lignocellulosic biomass (miscanthus and maple) and rich medium (malt extract agar). After five weeks of growth by the fungus on the biomass, the fungal RNA was extracted from three biological replicates per biomass type and mRNA was sequenced (approximately 30 million reads per sample). The reads were processed using ArrayStar to covert to RPKM and annotated using JGI's T. versicolor GO annotation file along with NCBI's BLAST. Comparisons were made between average gene expression of the fungus grown on maple, miscanthus, and the malt extract plate. A cut-off of 20X or greater expression was used for comparing fungi grown on either miscanthus or maple to the plate, with 45 and 61 transcripts meeting this threshold, respectively. The majority of the genes were known to be involved with biomass deconstruction by fungi (e.g. peroxidases, glycosyl hydrolases) with some unexpected genes appearing (e.g. MAPKKK). When comparing miscanthus with maple, a cut-off of 3X or greater expression was used giving 55 transcripts that were higher in maple and 46 transcripts that were higher in miscanthus. As with the previous comparisons with the rich media, most of the differentially expressed genes belonged to expected categories of enzymes involved in lignocellulose breakdown; however, it is notable that the majority of transcripts more highly expressed in miscanthus when compared to maple (at a 3X threshold) had unknown functions. Overall, this research provided insight into the biochemical mechanisms used by T. versicolor to deconstruct lignocellulosic biomass, and identified a plethora of uncharacterized genes encoding enzymes that may be critically important in lignocellulosic degradation.

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