Based on the publication “Adaptation of the pine fungal pathogen Grosmannia clavigera to monoterpenes: Biochemical mechanisms revealed by RNA-seq analysis,” Kligun et al.; DOI: 10.1111/efp.12372. The blue stain fungus Grosmannia clavigera is a fungal pathogen of coniferous trees that can tolerate monoterpenes of the oleoresin. The pathogen is rapidly spreading carried by the pine beetle that penetrates the tree bark and deposits its larvae in the tree core. The symbiotic relationship between the larvae and the fungi helps the larvae survive the toxic monoterpenes produced by the tree. Eventually, the fungi spreads in the tree blocking the flow of vital liquids and causing the tree to die.
This project is a good example of a mechanistic study in a non-model organism, showing how gene expression in G. clavigera promotes adaptation and which genes facilitate detoxification of monoterpenes and their utilization as a source of carbon and energy.
Next Generation Sequencing data was taken from the GEO database provided by a research group from the University of British Columbia (Vancouver, Canada) (Wang et al., 2013, 2014), GEO accession number GSE43006. Reference to files on the T-BioInfo server (SVL): http://tbioinfopb.pine-biotech.com/project-and-tutorial/rna-seq-analysis-tutorial-grosmannia-clavigera/
- Error Correction (eMER)
- Mapping on Genome (Non-model organism)
- Exon Detection (BS-Exon)
- Quantification of Expression (RSEM)
- Quantile Normalization
- Principal Component Analysis
- Two-way Clustering
Several newly detected transcripts annotated as putative retrotransposons were upregulated mostly under early-time-point terpene treatment, while others annotated as putative ribonuclease and protease were downregulated mostly during early-time-point terpene treatment. Based on these results, it can be hypothesized that these new transcripts could play a role in previously unidentified G. clavigera terpene response regulatory mechanisms. Overall, this study identified gene expression regulations supported by two data sets as well as new putative transcripts related to new processes that might be important for G. clavigera tolerance to terpenes.