{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE314nnn/GSE314252/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Solanum lycopersicum"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE314252"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Decoding stage-specific symbiotic programs in the Rhizophagus irregularis – tomato interaction using single-nucleus transcriptomics","description":"Arbuscular mycorrhizal fungi (AMF) establish a dynamic and asynchronous symbiosis with a wide range of land plants, involving distinct stages of root colonization and associated cellular responses that co-occur within the same root. 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. Together, our data support novel hypotheses on how diverse plant developmental and physiological pathways—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.","dates":{"publication":"2026/06/15"},"accession":"GSE314252","cross_references":{"GSM":["GSM9386792","GSM9386794","GSM9386793","GSM9386796","GSM9386795","GSM9386797"],"GPL":["27957"],"GSE":["314252"],"taxon":["Solanum lycopersicum"]}}