Fig. 7: Acoel and algal responses are coupled at late stages of regeneration.

Number of DEGs in acoel (a) and algae (b) at 1 and 2 dpa (log₂FoldChange \(\geqq\) 0.8 or \(\leqq\) −0.8 for upregulated and downregulated genes, respectively, p-adj \(\leqq\) 0.05; calculated with DESEQ2 using Wald test followed by Benjamini and Hochberg correction), in control and Cl-runt RNAi treated animals, which have drastically reduced numbers of DEGs. c Comparison of log₂FoldChange (log₂FC) for DEGs at 3 hpa and 2 dpa for algae (top) and acoel (bottom), showing minimum overlap between the early and late responses. Photosynthesis related genes, highlighted in green, are mostly only upregulated at 3 hpa. A set of algal TFs are differentially regulated only at 2 dpa, highlighted in blue. Black circles: genes differentially expressed at both time points (n = 12 for algae, n = 22 for acoel). d Heatmap reporting z-scores from triplicates of selected algal genes at 1 and 2 dpa. All genes shown were found differentially expressed (p-adj \(\leqq\) 0.05) between 2 and 0 dpa control RNAi samples or between Cl-runt and control RNAi samples at 2 dpa. The TFs correspond to those highlighted in blue in (c). e Schematic of proposed Cl-runt-mediated coordination between acoel and algal responses during regeneration. Dark gray arrows indicate responses dependent on Cl-runt activation. Activation of algal responses that are dependent on Cl-runt should be regulated indirectly through intercellular communication. The light gray, dashed arrows represent alternative pathways that may be activated during regeneration and influence algal responses in a Cl-runt-independent manner.