WGCNA
We were firstly interested in which factors impacted the gene expression
of Cladocopium and Durusdinium symbionts the most. To find
this out we identified groups of genes (“modules”) that were
co-regulated across samples using weighted gene co-expression network
analysis (WGCNA). These modules, which WGCNA identifies in an
unsupervised fashion without knowledge of the experimental design, are
then examined for correlation with known traits or experimental
treatments. In this way, it is possible to identify the largest and most
responsive groups of genes and then investigate what biological effects
they track. By examining the modules’ behavior across samples (Fig. 1)
we observed that the greatest gene expression difference in the
symbionts was not between “genus-background” and “genus-dominant”
states, as we initially expected. Instead, in both genera the most
distinct state was when the proportions of the two symbionts were near
equal within the host (Fig. 1), the state that we here term
“codominance.”
For Cladocopium, WGCNA identified nine modules of co-regulated
genes. Two of these modules, containing 1233 and 131 genes respectively,
were significantly correlated with codominance (r = 0.43, p <
4e-09 & r = 0.76, p < 2e-33). Additionally, the module
containing 131 genes was negatively correlated with the dominance ofCladocopium (r = -0.26, p < 5e-04). ForDurusdinium , WGCNA identified 7 modules of co-regulated genes.
Two of these modules, containing 815 and 81 genes respectively, were
significantly correlated with codominance (r = 0.71, p < 9e-25
& r = 0.3, p < 8e-05). One module, containing 5671 genes was
negatively correlated with codominance (r = -0.28, p < 2e-04).
Notably, neither symbiont had modules significantly associated with
exposure to elevated temperature.