Fig. 2

Pseudotime analysis showing differentially expressed gene modules. A Pseudotemporal ordering of nuclei along the two trajectories calculated from trajectory-specific (t = 0) points. Nuclei from four treatments (Virgin-Uninfected (VU), Virgin-Infected (VI), Mated-Uninfected (MU), and Mated-Infected (MI)) separate at different pseudo-time scales. The trajectories from infected nuclei are completely disjointed from the trajectories of uninfected nuclei, revealing a rapid and dramatic response to infection. B Monocle-based trajectory analysis separated nuclei along the two trajectories, colored by their cluster identity (from Fig. 1B), showing that only fat body nuclei are present in both trajectories. Other cell types such as oenocytes and muscle cells are present in Trajectory 1 and hemocytes are present in Trajectory 2, indicating these cell types do not have a strong transcriptional response to infection. C UMAP of Module 13 (Trajectory 1) and Module 16 (Trajectory 2) showing low gene aggregate expression scores for Mated-Uninfected (Trajectory 1) and Mated-Infected (Trajectory 2) compared to Virgin-Uninfected and Virgin-Infected, respectively. Gradient of color represents the aggregate expression score with bright color indicating a higher aggregate expression score. Each dot represents a single nucleus. GO term analysis showed enrichment for ribosome biogenesis in the two modules (Additional files 7 and 8, Additional file 1: Fig. S8)