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

Plant-parastic nematodes cause substantial crop losses worldwide. The sedentary endoparasite nematode Heterodera schachtii induces specialized feeding structures in host roots. The molecular mechanisms underlying feeding structure initiation and development remain poorly understood. High-resolution, spatially resolved transcriptomics is required to study localized gene expression patterns underlying feeding structure formation. Here, we introduce RNA tomography for plants, a powerful untargeted spatial transcriptomics technology that allows studying gene expression at cellular resolutions. We applied RNA tomography to Arabidopsis thaliana roots infected with H. schachtii at 1 and 2 days post inoculation. Our findings provide novel insights into early nematode parasitism. Four-day-old Arabidopsis seedlings grown in RoPod microscopic chambers were inoculated with ~20 H. schachtii infective stage juveniles (J2) per 3 seedlings. Roots with a single nematode infection at 1 and 2 days post inoculation were selected for RNA tomography library preparation.