Fig. 6: Spatially resolved R. irregularis transcripts reveal novel AM-specific gene expression patterns.

a, A single root cross-section within capture area (left) and overlapping distributions of all R. irregularis transcript expression (right) visualized in Loupe Browser. i, A representative root cross-section from a mycorrhizal capture area lacking recognizable fungal structures shows low expression of R. irregularis transcripts. ii, A representative root cross-section from a mycorrhizal capture area that contains visible arbuscules (red arrows) shows high expression of R. irregularis transcripts, particularly around arbuscules (scale bar, 250 µm; scale, log(UMI counts + 1)). Approximately 50 root cross-sections across nine mycorrhizal-treated capture areas were analysed. b, A dot plot of RiEF1α and various transporters utilizing hierarchical clustering within integrated mycorrhizal spatial object. c, A dot plot of RiEF1α and various effector proteins utilizing hierarchical clustering within the integrated mycorrhizal spatial object. d, A bar plot depicting top 25 Gene Ontology categories for all expressed R. irregularis transcripts (biological process (i), molecular function (ii) and cellular component (iii)).