Profiling the Cannabis-Sclerotinia pathosystem at the mRNA level using dual RNA sequencing

Known to infect more than 600 plant species worldwide, Sclerotinia sclerotiorum is a necrotrophic fungal pathogen, and the causative agent of white mold. With recent infection reports documented across North America, Cannabis sativa is known to be susceptible to Sclerotinia infection. Resulting from legal constraints associated with C. sativa, little is known about the Cannabis-Sclerotinia pathosystem, particularly in how the plant responds to pathogen attack at the cellular and molecular levels. Anatomical study revealed initial infection and degradation of the epidermis and cortical parenchyma, followed by widespread infection of the vascular phloem. Dual RNA sequencing provided a detailed transcriptomic profile of this pathosystem directly at the site of infection. Differential gene expression analysis revealed large-scale transcriptional shifts resulting from rapid infection. We identified the upregulation of 97 genes at 1 day post inoculation (dpi) and 6733 genes 5 dpi in C. sativa, while 3186 genes were identified in S. sclerotiorum 7 dpi. Gene ontology term enrichment identified processes associated with plant defense and signal transduction cascades during C. sativa infection while processes associated with redox control and sugar catabolism were enriched in S. sclerotiorum. Taken together, this study revealed transcriptional reprogramming in both the host plant and fungal pathogen associated with degradation of host cortical and vascular phloem tissues. Overall design: Cannabis sativa (cultivar 'Kona') inflorescences were inoculated with Sclerotinia sclerotiorum. Infected and uninfected tissues were collected at 1 day post inoculation (dpi), 3 dpi, 5 dpi and 7 dpi.