Metatranscriptomic analyses of grapes reveal differences in expressed functional genes of filamentous and yeast fungi during noble rot and grey rot

Abstract

Botrytis cinerea is a necrotrophic fungus causing grey rot (GR) with crucial economic losses in fruit crops. It can also cause the desired noble rot (NR) in grape berries used to produce botrytized wines. In both states, B. cinerea is associated with several other fungi, but the functional role of these is still poorly understood. Metatranscriptomic data was generated from healthy (H), noble rot (NR) and grey rot (GR) grape berries and RNA-seq reads were aligned to the most prevalent filamentous fungi and yeasts based on previous culture-based studies. Differential enrichment analyses and pathway enrichment analyses revealed that all filamentous fungi and yeasts are most active in NR, besides GR and H berries. Beside B. cinerea, several functional genes of other fungi were linked to well-known physico-chemical changes in NR berries and to the production of antagonistic interaction genes. Our study demonstrates the complex interaction dynamics of the grape microbiome.