DOI: 10.5061/dryad.k3j9kd57b
title: Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

description: 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.
description: 685, 205 <i>Siderastrea radians</i> host
 transcriptome Fasta file of the assembled sequences
 from <em>Siderastrea radians </em>host from El Islote, Puerto
 Morelos, Mexico. 173, 968 <em>Siderastrea
 radians</em> photosymbiont transcriptome  Fasta
 file of the assembled sequences from <em>Siderastrea
 radians</em> photosymbiont <i>Breviolum
 </i>'B5' from El Islote Puerto Morelos, Mexico.
 58,038 <em>Siderastrea radians</em> bacterial
 transcriptome  Fasta file of the assembled sequences
 from <em>Siderastrea radians </em>associated bacterial
 communities<em> </em>from El Islote Puerto Morelos,
 Mexico. 731, 432 <em>Pseudodiploria
 clivosa</em> host transcriptome Fasta file of
 the assembled sequences from <em>Pseudodiploria clivosa</em>
 host from La Bocana Puerto Morelos, Mexico. 184,
 910 <em>Pseudodiploria clivosa</em>
 photosymbiont transcriptome Fasta file of the
 assembled sequences from <em>Pseudodiploria
 clivosa</em> photosymbiont <i>Breviolum
 faviinorum</i> from La Bocana Puerto Morelos, Mexico.
 3,182 <em>Pseudodiploria clivosa</em> bacterial
 transcriptome  Fasta file of the assembled sequences
 from <em>Pseudodiploria clivosa </em>associated bacterial
 communities<em> </em>from La Bocana Puerto Morelos,
 Mexico. <strong>913, 821 <em>Orbicella
 faveolata </em>host transcriptome </strong>
 Fasta file of the assembled sequences from <em>Orbicella
 faveolata</em> host from La Bocana Puerto Morelos, Mexico.
 202, 193 <em>Orbicella faveolata</em>
 photosymbiont transcriptome Fasta file of the
 assembled sequences from <em>Orbicella faveolata</em>
 photosymbiont <em>Symbiodinium</em> 'A3' from La
 Bocana Puerto Morelos, Mexico. 5,
 239 <em>Orbicella faveolata</em> bacterial
 transcriptome  Fasta file of the assembled sequences
 from <em>Orbicella faveolata </em>associated bacterial
 communities<em> </em>from La Bocana Puerto Morelos,
 Mexico. Gene Name Annotations for <i>Siderastrea
 radians</i> host transcriptome .tab file of gene
 name annotations for transcripts in the <em>Siderastrea
 radians</em> host transcriptome. Gene Name
 Annotations for <em>Siderastrea
 radians</em> photosymbiont transcriptome .tab
 file of gene name annotations for transcripts in the
 <em>Pseudodiploria clivosa</em> photosymbiont
 <em>Breviolum </em>'B5' transcriptome.
 Gene Name Annotations for <i>Siderastrea
 radians</i> bacterial transcriptome .tab file of
 gene name annotations for transcripts in the <em>Siderastrea
 radians</em> associated bacterial
 communities transcriptome. Gene Name Annotations for
 <i>Pseudiploria clivosa</i> host transcriptome
 .tab file of gene name annotations for transcripts in the
 <em>Pseudodiploria clivosa</em> host transcriptome.
 Gene Name Annotations for <em>Pseudodiploria
 clivosa</em> photosymbiont transcriptome .tab
 file of gene name annotations for transcripts in the
 <em>Pseudodiploria clivosa</em> photosymbiont
 <em>Symbiodinium </em>'A3' transcriptome.
 Gene Name Annotations for <em>Pseudodiploria
 clivosa</em> bacterial transcriptome .tab file
 of gene name annotations for transcripts in the <em>Pseudodiploria
 clivosa</em> associated bacterial
 communities transcriptome. Gene Name Annotations for
 <em>Orbicella faveolata</em> host transcriptome
 .tab file of gene name annotations for transcripts in the
 <em>Orbicella faveolata</em> host transcriptome.
 Gene Name Annotations for <em>Orbicella
 faveolata</em> photosymbiont transcriptome .tab
 file of gene name annotations for transcripts in the <em>Orbicella
 faveolata</em> photosymbiont <em>Symbiodinium
 </em>'A3' transcriptome. Gene Name
 Annotations for <em>Orbicella faveolata</em> bacterial
 transcriptome .tab file of gene name annotations for
 transcripts in the <em>Orbicella faveolata</em> associated
 bacterial communities transcriptome. <b>Scripts
 for analyzing ITS2 Symbiodiniaceae Next-Generation Sequencing Amplicon
 Data </b> Annotated scripts for completing
 Symbiodiniaceae genotyping analyses as described in the publication,
 included ITS2 Symbiodiniaceae raw read files.
 <b>Scripts for analyzing gene expression evolution (EVE)
 and EVE method variants (EVE-R, EVE-ReSt) </b>
 Annotated scripts for the Expression variance and evolution model
 and method variants as described in the publication.
 <b>Host input ortholog expression matrix for analyzing gene
 expression evolution (EVE-R) </b> Combined gene
 expression matrix for the three coral species used as input for the
 EVE/EVE-R method as described in the publication.
 <b>Photosymbiont input ortholog expression matrix for
 analyzing gene expression evolution (EVE-R) </b>
 Combined gene expression matrix for the three photosymbiont
 species used as input for the EVE/EVE-R method as described in the
 publication. <b>Host input ortholog expression
 matrix for analyzing gene expression evolution
 (EVEReSt) </b> Combined gene expression matrix
 for the three coral species used as input for the EVEReSt method as
 described in the publication.
 <b>Photosymbiont input ortholog expression matrix for
 analyzing gene expression evolution (EVEReSt) </b>
 Combined gene expression matrix for the three photosymbiont
 species used as input for the EVEReSt method as described in the
 publication.