Genome assembly for Mycena citricolor the causal agent of the American Leaf Spot

Mycena citricolor is a phytopathogenic fungus that causes the American Leaf Spot (ALS), a disease in a broad range of hosts and crops, including coffee and avocado. This hemibiotroph fungus penetrates the plant through damage induced by oxalic acid secreted by asexual structures (gemma). In coffee, it causes 20-90% crop losses depending on the environment and production system conditions. M. citricolor is the only known pathogenic species in the Mycena genus, which comprises a large group of mushroom-shaped saprophytic fungi. We believe that differences in their lifestyle, saprophytic versus pathogenic, are reflected in their genome, and understanding these differences can help us to identify the genetic machinery associated with infection. There are currently no ALS-resistant cultivars, particularly coffee, and their development can be accelerated by a better understanding of the pathogen strategies to cause ALS. To identify pathogenicity-related genes in M. citricolor, we used protein family copy-number variation, secretome prediction, and homology to known virulence factors in two M. citricolor genome assemblies, including a newly assembled and annotated long-read reference genome.