As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.

685, 205 Siderastrea radians host transcriptome

Fasta file of the assembled sequences from Siderastrea radians host from El Islote, Puerto Morelos, Mexico.

173, 968 Siderastrea radians photosymbiont transcriptome 

Fasta file of the assembled sequences from Siderastrea radians photosymbiont Breviolum 'B5' from El Islote Puerto Morelos, Mexico.

58,038 Siderastrea radians bacterial transcriptome 

Fasta file of the assembled sequences from Siderastrea radians associated bacterial communities from El Islote Puerto Morelos, Mexico.

731, 432 Pseudodiploria clivosa host transcriptome

Fasta file of the assembled sequences from Pseudodiploria clivosa host from La Bocana Puerto Morelos, Mexico.

184, 910 Pseudodiploria clivosa photosymbiont transcriptome

Fasta file of the assembled sequences from Pseudodiploria clivosa photosymbiont Breviolum faviinorum from La Bocana Puerto Morelos, Mexico.

3,182 Pseudodiploria clivosa bacterial transcriptome 

Fasta file of the assembled sequences from Pseudodiploria clivosa associated bacterial communities from La Bocana Puerto Morelos, Mexico.

913, 821 Orbicella faveolata host transcriptome 

Fasta file of the assembled sequences from Orbicella faveolata host from La Bocana Puerto Morelos, Mexico.

202, 193 Orbicella faveolata photosymbiont transcriptome

Fasta file of the assembled sequences from Orbicella faveolata photosymbiont Symbiodinium 'A3' from La Bocana Puerto Morelos, Mexico.

5, 239 Orbicella faveolata bacterial transcriptome 

Fasta file of the assembled sequences from Orbicella faveolata associated bacterial communities from La Bocana Puerto Morelos, Mexico.

Gene Name Annotations for Siderastrea radians host transcriptome

.tab file of gene name annotations for transcripts in the Siderastrea radians host transcriptome.

Gene Name Annotations for Siderastrea radians photosymbiont transcriptome

.tab file of gene name annotations for transcripts in the Pseudodiploria clivosa photosymbiont Breviolum 'B5' transcriptome.

Gene Name Annotations for Siderastrea radians bacterial transcriptome

.tab file of gene name annotations for transcripts in the Siderastrea radians associated bacterial communities transcriptome.

Gene Name Annotations for Pseudiploria clivosa host transcriptome

.tab file of gene name annotations for transcripts in the Pseudodiploria clivosa host transcriptome.

Gene Name Annotations for Pseudodiploria clivosa photosymbiont transcriptome

.tab file of gene name annotations for transcripts in the Pseudodiploria clivosa photosymbiont Symbiodinium 'A3' transcriptome.

Gene Name Annotations for Pseudodiploria clivosa bacterial transcriptome

.tab file of gene name annotations for transcripts in the Pseudodiploria clivosa associated bacterial communities transcriptome.

Gene Name Annotations for Orbicella faveolata host transcriptome

.tab file of gene name annotations for transcripts in the Orbicella faveolata host transcriptome.

Gene Name Annotations for Orbicella faveolata photosymbiont transcriptome

.tab file of gene name annotations for transcripts in the Orbicella faveolata photosymbiont Symbiodinium 'A3' transcriptome.

Gene Name Annotations for Orbicella faveolata bacterial transcriptome

.tab file of gene name annotations for transcripts in the Orbicella faveolata associated bacterial communities transcriptome.

Scripts for analyzing ITS2 Symbiodiniaceae Next-Generation Sequencing Amplicon Data 

Annotated scripts for completing Symbiodiniaceae genotyping analyses as described in the publication, included ITS2 Symbiodiniaceae raw read files.

Scripts for analyzing gene expression evolution (EVE) and EVE method variants (EVE-R, EVE-ReSt) 

Annotated scripts for the Expression variance and evolution model and method variants as described in the publication.

Host input ortholog expression matrix for analyzing gene expression evolution (EVE-R) 

Combined gene expression matrix for the three coral species used as input for the EVE/EVE-R method as described in the publication.

Photosymbiont input ortholog expression matrix for analyzing gene expression evolution (EVE-R) 

Combined gene expression matrix for the three photosymbiont species used as input for the EVE/EVE-R method as described in the publication.

Host input ortholog expression matrix for analyzing gene expression evolution (EVEReSt) 

Combined gene expression matrix for the three coral species used as input for the EVEReSt method as described in the publication.

Photosymbiont input ortholog expression matrix for analyzing gene expression evolution (EVEReSt) 

Combined gene expression matrix for the three photosymbiont species used as input for the EVEReSt method as described in the publication.