Fig. 1: Overview of Experimental Design and Analysis.

a Summary of the SCTLD transmission experiment in which eight replicates of five susceptible coral species were split in half, with one half exposed to a healthy D. labyrinthiformis colony (control) and the other half exposed to a diseased D. labyrinthiformis colony (disease). The control panel names the species in the study, and the disease panel shows the resulting species-level disease phenotypes used to inform our statistical analyses. b Venn Diagram showing the number of unique and shared DEGs across species between control and disease treatments. The total number of DEGs within each species was enumerated as well as the number and percentage of those involved in immunity and viral response. c EVE model summary for host orthologs. 1766 single-copy orthologs were identified across the five species in our study and their expression was used as inputs for the EVE model used to differentiate genes with lineage-specific and highly variable expression. Pearson correlations were run on lineage-specific orthologs to identify those correlated to disease phenotypes, and one-way ANOVAs followed by TukeyHSD tests were run on highly variable orthologs to identify those with significant differential expression between disease states. d Symbiont composition determined by binning RNAseq reads to Symbiodinium (S), Breviolum (B), Cladocopium (C) and Durusdinium (D) reference transcriptomes. The first panel shows symbiont genera composition pie charts averaged across samples within each species. The second panel shows the dominant symbiont present within each sample. The expression from these dominant symbionts were used for downstream analyses. e Venn Diagram showing the number of unique and shared DEGs across dominant symbionts between control and disease treatments. The total number of DEGs within each was enumerated as well as the number and percentage of those involved in the relevant process of photosynthesis. f EVE model summary for dominant symbiont orthologs. 5125 single-copy orthologs were identified across symbiont genera and their expression was used as input for the EVE model. Pearson correlations were run on lineage-specific orthologs to identify those correlated to disease phenotypes, and one-way ANOVAs followed by TukeyHSD tests were run on highly variable orthologs to identify those with significant differential expression between disease states. (cnat Colphophyllia natans, oann Orbicella annularis, pstr Pseudodiploria strigosa, past Porites astreoides, mcav Montastraea cavernosa, LGR Lesion Growth Rate, RR Relative Risk, ECM Extracellular Matrix, EVE Expression Variance and Evolution).