biostudies-literatureSerrano KDOE | SC | Biological and Environmental ResearchDOE | LDRD | Lawrence Berkeley National LaboratoryDOE | SC | Biological and Environmental Research (BER)673-688https://www.ebi.ac.uk/biostudies/studies/S-EPMC11035146biostudies-literatureUnknown10(4)The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptomNature plantsSpatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis.PMC11035146DE-AC02-05CH11231Malmstrom RRVisel AScheller HVCole BO'Malley RSerrano KBezrutczyk MDao TGoudeau DfalseSpatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis.The symbiotic interaction of plants with arbuscular mycorrhizal (AM) fungi is ancient and widespread. Plants provide AM fungi with carbon in exchange for nutrients and water, making this interaction a prime target for crop improvement. However, plant-fungal interactions are restricted to a small subset of root cells, precluding the application of most conventional functional genomic techniques to study the molecular bases of these interactions. Here we used single-nucleus and spatial RNA sequencing to explore both Medicago truncatula and Rhizophagus irregularis transcriptomes in AM symbiosis at cellular and spatial resolution. Integrated, spatially registered single-cell maps revealed infected and uninfected plant root cell types. We observed that cortex cells exhibit distinct transcriptom2024-01-01T00:00:00Z2024 Apr2026-06-01T19:59:49.673Z2026-05-20T03:08:31.486ZS-EPMC110351463858948510.1038/s41477-024-01666-3