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.