Genome-wide characterisation of pathogenicity-related proteins inMycena citricolor,the causal agent of the American Leaf Spot in coffee

Abstract

AbstractMycena citricoloris a fungus that causes the American Leaf Spot (ALS) disease in multiple hosts, including coffee and avocado. This hemibiotroph penetrates the plant through damage induced by oxalic acid. This can cause 20-90% crop losses in coffee depending on the environmental and production conditions.M. citricoloris the only known pathogenic species in theMycenagenus, a large group of saprophytic mushrooms. Comparing the saprophytic and pathogenic genomes can allow us to identify genetic machinery associated with the pathogen’s genome-wide functional acquisitions to cause disease.To identify pathogenicity-related genes inM. citricolor, we analysed protein family copy-number variation, secretome prediction, and homology to known virulence factors in twoM. citricolorassemblies, including a newly assembled and annotated long-read genome. We found that the pathogenicM. citricolorhad a higher proportion of secreted genes expanded in copy-number, and expanded gene copies homologous to known virulence factors than the saprophyticMycena. We shortlisted over 300 candidate genes in eachM.citricolorassembly. Focusing on genes strongly regulated during plant interaction, we found over 100 candidates, primarily from multiple copies (up to 4-3 times) of 42 well-known virulence factors (e.g. MFS1, CUTA, NoxA/B, OLE1, NorA), plus a few clade-specific uncharacterised genes.M.citricolortransition to a pathogenic lifestyle reflected genome-wide functional changes.M.citricolorseems to primarily depend on well-known virulence factors in large copy numbers, suggesting the molecular plant-interaction processes involved are like those of better-studied fungi. Hypothetically, the development of ALS resistance could mirror studied responses to these virulence factors.