Leveraging Single-Cell and spatial multi-Omics to unravel the molecular interPlay bEtween Botrytis cinerea and strawbERRY flowers and fruit

2026-07-22

Botrytis cinerea, a necrotrophic fungus that causes grey mold, poses a significant pre- and post-harvest threat to 1.2 million tonnes of strawberry produced annually in the EU. This pathogen can establish quiescent, asymptomatic infections in strawberry flowers and unripe fruit, which progress to symptomatic infections as the fruit ripens. Despite its importance, the biological and environmental factors that regulate the onset and termination of B. cinerea quiescence remain poorly understood. In this study, I propose an interdisciplinary approach combining microscopy, molecular biology, and transcriptomics to unravel mechanisms driving quiescent infections and host susceptibility in the B. cinerea-strawberry pathosystem. First, I will use confocal fluorescence microscopy to track B. cinerea infection in strawberry flowers and fruit, visualizing the pathogen’s entry and transition from quiescence to necrotrophic disease. Building on these observations, I will apply single-nucleus and spatial RNA sequencing to profile the transcriptomes of both the pathogen and host at cellular resolution during key phases of infection. The resulting data will be integrated and analyzed using cutting-edge bioinformatic tools to explore cellular diversity in both organisms and identify the host's transcriptional responses during infection, providing new insights into the molecular pathways governing the complex B. cinerea-strawberry interaction. This research pioneers the use of single-nucleus and spatial transcriptomics to study host-pathogen interactions, overcoming challenges in detecting and profiling invading pathogens at the single-cell level, and application to non-model plant species. It leverages my expertise in plant genetics, the host lab’s specialty in molecular interactions, and collaborators’ proficiency in single-cell technology and microscopy, creating a powerful professional network that will drive the success of the project and support my career growth.

Belgium

2026-01-01