Decoding powdery mildew genetics to breed disease-resistant cannabis

Cannabis powdery mildew, caused by the fungal pathogen Golovinomyces ambrosiae, poses a significant threat to licensed producers as its presence on marketable products can compromise product innocuity. While there is a focus in research for resistance genes within the Cannabis sativa germplasm, there is a lack of genetic information regarding the infecting agent, preventing validation of their effectiveness against different populations as the plant-pathogen interaction most likely follows a gene-for-gene relationship. In this paper, we assembled the first G. ambrosiae genome, providing insights into its genomic content and potential virulence determinants. The assembly was made using a hybrid approach, combining Oxford Nanopore Technologies long reads and Illumina short reads. The resulting 155.2 Mb genome is composed of 73 contigs, 13 scaffolds and has a completeness score of 97.5%. Subsequent analysis highlighted the substantial transposable elements content of the pathogen, occupying 82.64% of its genomic composition. Prediction of protein-coding genes revealed 6995 highly confident gene models, including 169 candidate effector proteins. Among the latter, we highlighted 14 candidates sharing key characteristics of confirmed effectors in other powdery mildew pathosystems such as the presence of signal peptides, RALPH-like domains, and Y/F/WxC motifs. The result of this study provides valuable resources for future identification of avirulence genes within the G. ambrosiae species, responsible of conferring resistance when encoded effectors are recognized by a cognate host's resistance genes. Those findings will lead to guided breeding strategies and, ultimately, the selection of cultivars adapted to the pathogen's virulence profile.