Weighted gene coexpression network analysis
This analysis (WGCNA) (Langfelder & Hovarth, 2008) was used to identify groups of co-regulated genes in both symbiont genera, to explore major patterns of gene expression variation in an unsupervised way. The input for this analysis were the matrices of normalized variance stabilized counts obtained with R function DESeq2::vst(), from which the variation due to study and to the logarithm of total read count was removed using the R function limma::removeBatchEfect. For Cladocopium , we ran WGCNA with a soft threshold power of 10, a minimum module size of 30, and a module merging threshold of 0.4. For Durusdinium , we ran WGCNA with a soft threshold power of 12, a minimum module size of 30, and a module merging threshold of 0.4.