(A) Camera images show the secondary plasmodium before and after sampling a fan- and network-enriched sample (encircled by black lines), respectively, for the snRNA-seq experiment. (B) Histograms visualize transcript (bottom) and gene (top) detection counts per nucleus for each plasmodium sampled. Center: feature plots show transcript detection counts on Uniform Manifold Approximation and Projection (UMAP) embedding. (C) Heatmap representation of marker gene expression for primary plasmodium clusters shown in Figure 4B. (D) Heatmap representation of marker gene expression for secondary plasmodium clusters shown in Figure 4E. (E) Sporulation score is shown as a feature onto the UMAP embedding in Figure 4E. The score was estimated as the sum of transcript counts for a list of fruiting body formation specific genes (Glöckner and Marwan, 2017). (F) UMAP embedding and clusters (indicated by different colors) obtained by excluding unannotated transcripts (total: 14,055 transcripts) for the primary plasmodium as shown in Figure 3B (left). The same nuclei were embedded by using all transcripts (total: 24,592 transcripts) with different colors representing the clusters in Figure 3B (right). (G) UMAP embedding and clusters (indicated by different colors) obtained by excluding unannotated transcripts (total: 14,483) for the secondary plasmodium (see Figure 3E) (left). The same nuclei were embedded by using all transcripts (total: 25,815) with different colors representing the clusters in Figure 3E (right). (H) Primary plasmodium-specific Gene Ontology (GO) enrichments (right) obtained by using GOseq on cluster-specific marker genes (see Figure 3B and inset bottom left; Young et al., 2010) are visualized as dotplots using Revigo (Supek et al., 2011) with dot distances reflecting similarity of GO terms. Bold letters highlight shared terms between primary plasmodium and SM1. (I) Dotplot visualization of GO enrichments for the secondary plasmodium as described in (B) (right). Bold letters highlight shared terms between the secondary plasmodium and SM4. See Figure 3E and inset (bottom left) for more cluster information.