RNA tomography reveals spatial gene expression maps of Arabidopsis thaliana roots infected with Heterodera schachtii

Summary Plant‐parasitic cyst nematodes, such as Heterodera schachtii , cause substantial crop losses world‐wide and induce specialized feeding structures in host roots, yet the molecular mechanisms underlying feeding structure initiation and development remain poorly understood. We introduce RNA tomography for plants, a powerful untargeted spatial transcriptomics technology that allows studying gene expression at high spatial resolution. We applied RNA tomography to Arabidopsis ( Arabidopsis thaliana ) roots infected with H. schachtii , capturing 96 consecutive cross sections of 20 micrometers at 1‐ and 2‐d post inoculation (dpi). We identified the location of the nematode's pharyngeal glands, the organs where most effectors are produced, using marker genes, and discovered multiple uncharacterized H. schachtii genes expressed in the same region. Additionally, we mapped the Arabidopsis spatial gene expression response upon nematode infection, revealing that some genes are expressed in a specific section. Our findings provide novel insights into early nematode parasitism. RNA tomography offers a powerful new approach to understanding plant cellular organization and interactions under various conditions, including development and responses to biotic and abiotic stresses.