Decoding stage-specific symbiotic programs in the Rhizophagus irregularis – tomato interaction using single-nucleus transcriptomics

Whilst decades of research have significantly enhanced 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 clustering of an AM-specific cluster reveals AM-responsive root epidermal cells as well as a developmental gradient of cortical cells across distinct stages of arbuscule formation, unveiling colonization stage-specific transcriptional signatures. 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.