Fig. 5: Existing and novel transcriptomic studies reveal a robust set of differentially expressed M. truncatula genes during the AM symbiosis.

a, A Venn diagram showing overlap in symbiosis-responsive M. truncatula genes with a log fold change > or <1 between the spatial dataset from this study and the two previously published LCM RNA-seq studies from Gaude et al.¹⁵ and Hogekamp et al.¹⁴. b, The breakdown of predicted cell types represented in each cluster within the integrated spatial dataset in terms of number of voxels. DEGs between mycorrhizal and control treatments are shown above each bar for each cluster, with the counts of significantly (Sig; see Methods) upregulated M. truncatula genes in red and downregulated gene counts in blue. c, The expression of four canonical pre- and post-AM symbiosis marker genes shown in a UMAP plot of single-nuclei dataset (upper). The expression of four genes enriched in the CCC cluster of this dataset that have yet unknown roles in AMF colonization, shown in a UMAP plot of single-nuclei dataset (lower). The UMAP plots are coloured by normalized mRNA counts (scale, log(UMI counts + 1)) depending on the marker gene, thus reflecting the colonization stage.