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Spatial transcriptomics enables precise spatiotemporal analyses of gene expression, facilitating studies of cell heterogeneity. We performed spatial transcriptomic sequencing on Moneymaker tomato root galls caused by\n                    <jats:italic>M. incognita<\/jats:italic>\n                    infection at 3, 5, and 7\u00a0days post-inoculation to investigate RKN-induced giant cell formation. Five major cell types were identified; of these, giant cell clusters were localized predominantly in the xylem, stele, and meristem. Four novel giant cell-specific marker genes were confirmed through RNA in situ hybridization. Pseudotime analysis revealed genes potentially associated with giant cell formation. Virus-induced gene silencing (VIGS) of four genes encoding a cyclin-dependent kinase, two cell division cycle-associated proteins, and a MYB3R-1-like transcription factor\u2014hypothesized to maintain the cell cycle or gene expression during mitosis\u2014resulted in significantly fewer galls and significantly smaller giant cells. This study established the first spatiotemporal atlas of RKN-infected tomato roots and identified genes associated with giant cell formation, laying a foundation for further research on the establishment of RKN feeding sites, providing novel insights into RKN pathogenic mechanisms, and potentially guiding novel control strategies.\n                  <\/jats:p>","DOI":"10.1186\/s43897-026-00272-5","type":"journal-article","created":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T11:01:31Z","timestamp":1786446091000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A spatiotemporal atlas of giant-cell formation during Meloidogyne incognita infection in tomato roots"],"prefix":"10.1186","volume":"6","author":[{"given":"Lijun","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianqian","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runmao","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiangzhou","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kuai","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenyang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenzheng","family":"Ling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haichao","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert Y. 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