Creating a genomic resource for Grosmannia clavigera

Rapid advances in DNA sequencing have created the possibility for probing deeply into the genomes and transcriptomes of organisms; however, bioinformatic tools for handling these massive quantities of data are changing rapidly. In this thesis I describe the bioinformatic methods and molecular resources developed for studying the ascomycete fungus Grosmannia clavigera (Gc), a lodgepole pine (Pinus contorta) pathogen specifically associated with the Mountain Pine Beetle (MPB), and results from initial analyses using these resources. We have developed genomic resources for Gc including: a) the whole genome sequence, b) expressed sequence tags (ESTs), and c) RNA-seq data. We have annotated the genome using the transcriptome resources (e.g. ESTs and RNA-seq) and computational (gene prediction software) data. In an initial analysis of the Gc genome we focused on aspects important for colonizing the host tree and for tolerance towards conifer defence chemicals. We showed that Gc is heterothallic, and report evidence for repeat-induced point mutation. Gene expression profiling provided insight into mechanisms for Gc’s tolerance towards conifer defence chemicals, specifically oleoresin terpenoids. RNA-seq revealed a substantial antimicrobial stress response of Gc induced by terpenoids, and our data suggests that Gc may reduce the toxicity of these defence chemicals by utilizing them as a carbon source. Terpenoid treatment strongly activated a ~100 kb region of the Gc genome that contains a set of genes that may be important for detoxification of these host defence chemicals. Using a recently developed Gc gene knock-out system, we provide evidence that a PDR-type ABC transporter is important for the successful response of Gc against host terpenoids.Forestry, Faculty ofGraduat