Gene Ontology Analysis
To ascertain the functions of differentially expressed genes of symbionts in the codominant state, we used a Gene Ontology (GO) enrichment analysis that utilizes the Mann-Whitney U test (Wright et al., 2017). For Cladocopium symbionts, there were 2,019 differentially expressed genes (DEGs), with an FDR cut-off of 10%. At the GO level, the most notable signal pertained to ribosomes and photosynthesis. There were nine cellular component GO terms that were significantly (adjusted p < 0.001) enriched by upregulated genes. Of these, six were related to ribosome, and three to chloroplast (Fig. 2A).
We repeated the same analysis for Durusdinium symbionts, identifying 5,497 DEGs at the 10% FDR level. Like Cladocopium , the Durusdinium GO analysis results in multiple terms related to ribosomes and photosynthesis. There were ten cellular component terms that were significantly (adjusted p < 0.001) enriched by upregulated genes. Of these, seven were related to ribosomes and two to chloroplasts (Fig. 2B).
Lastly, we did this analysis for the coral host, identifying 7,799 DEGs at the 10% FDR level. Like the symbionts, there were multiple GO terms related to ribosomes. There were four cellular component terms that were significantly (adjusted p < 0.001) enriched by upregulated genes. Of these, three were related to ribosomes (Fig. 2C). Additionally, there were 11 GO terms significantly (adjusted p < 0.005) enriched for downregulated genes. Of these, six were related to neurons.