Decoding Stage-Specific Symbiotic Programs in the Rhizophagus Irregularis-Tomato Interaction Using Single-Nucleus Transcriptomics.

Arbuscular mycorrhizal fungi (AMF) establish a dynamic and asynchronous symbiosis with a wide range of land plants, which involves distinct stages of root colonization and associated cellular responses that co-occur within the same root. While decades of research have significantly advanced our understanding of the plant's symbiotic gene repertoire, this spatial and temporal complexity has hindered a detailed dissection of the molecular mechanisms underlying fungal accommodation. Here, we present the first single-nucleus RNA-sequencing (snRNA-seq) dataset of Solanum lycopersicum roots colonized by Rhizophagus irregularis. Unsupervised subclustering of an arbuscular mycorrhiza (AM)-specific cell population resolves AM-responsive root epidermal cells as well as a developmental gradient of cortical cells across distinct stages of arbuscule formation, thus unveiling stage-specific transcriptional signatures during AMF colonization. Moreover, using motif-informed network inference based on single-cell expression data (MINI-EX), we put forward candidate transcription factors orchestrating these stage-specific transcriptional programs. Together, our data support novel hypotheses on how diverse plant developmental and physiological processes-including localized cell-cycle reactivation and the integration of multiple nutritional cues-are coordinated to facilitate the establishment of a functional symbiosis. As such, this high-resolution dataset serves as a valuable resource for candidate gene prioritization and future reverse genetic studies.