This study tracked how desert truffles form a beneficial partnership with plant roots over 10 weeks, identifying three distinct stages with different structures and genetic activity patterns. Researchers used microscopy and gene analysis to understand how the fungus gradually colonizes the root system, starting with growth in soil, then spreading between root cells, and finally penetrating inside cells. The findings reveal that specific fungal and plant genes are active at different stages, particularly those involved in breaking down plant cell walls. This research helps explain how desert truffles can be cultivated more effectively for food production.