Figure 4.

Schematic of the RNA-seq analyses on colonies of the Caribbean coral O. faveolata collected during and after the 2010 coral bleaching in La Parguera, Puerto Rico. RNA-seq reads from all samples (n=12) were grouped together to built a reference transcriptome and then filtered with genomic and transcriptomic data from several Symbiodinium types, as well as with the O. faveolata genome, to generate expression profiles for the holobiont (i.e. metatranscriptome), ‘Symbiodinium spp.’, ‘O. faveolata’ and ‘other-eukaryotes’. ‘Orbicella faveolata’ profile shows a different pattern to that seen in the other profiles due to the clustering of the bleaching and unbleached colonies in separate groups. Letters next to the ‘Symbiodinium spp.’ profile depict the Symbiodinium type found in the sequenced colonies. Identities of Symbiodinium types were obtained with a BLAST alignment performed against ITS2 sequence data from types known to associate with the coral O. faveolata.