Comparison of GO term delta-ranks between symbiont genera
To compare the functional signals ofCladocopium and Durusdinium symbionts in response to codominance, we used the GO_MWU analysis results which output the degree of up- or down-regulation of GO terms as measured by the “delta-rank” – the difference between the median rank of the genes annotated with the term and the median rank of all other genes. In GO_MWU, a positive delta-rank implies up-regulation of genes annotated with the GO term. The comparison of delta ranks (rather than per-gene expression changes) between experiments integrates the signal over meaningful functional categories of genes and, importantly for the current study, circumvents the problem of different reference transcriptomes used. At the GO delta-rank level, responses ofCladocopium and Durusdinium to codominance were clearly similar (Fig. 3), although the statistical significance of this similarity cannot be formally ascertained because GO terms are not independent (they may encompass overlapping sets of genes). Most notably, ribosomal and photosynthesis categories were similarly and significantly (p < 0.001) enriched for upregulated genes in both genera. These GO categories include large ribosomal subunit, small ribosomal subunit, ribonucleoprotein complex, thylakoid part, photosystem, and plastid part (p < 0.001).