Sachs, J. L., Mueller, U. G., Wilcox, T. P. & Bull, J. J. The evolution of cooperation. Q. Rev. Biol. 79, 135–160 (2004).
Google Scholar
MeloClavijo, J., Donath, A., Serôdio, J. & Christa, G. Polymorphic adaptations in metazoans to establish and maintain photosymbioses. Biol. Rev. 93, 2006–2020 (2018).
Google Scholar
Wernegreen, J. J. Endosymbiosis. Curr. Biol. 22, 555–561 (2012).
Google Scholar
Heijtz, R. D. et al. Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. USA 108, 3047–3052 (2011).
Google Scholar
Schmidt, T. S. B., Raes, J. & Bork, P. The human gut microbiome: From association to modulation. Cell 172, 1198–1215 (2018).
Google Scholar
Morgan, X. C. et al. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 16, 67 (2015).
Google Scholar
Tromas, A. et al. Heart of endosymbioses: Transcriptomics reveals a conserved genetic program among arbuscular mycorrhizal, actinorhizal and legume-rhizobial symbioses. PLoS One 7, 1–7 (2012).
Chun, C. K. et al. An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genom. 7, 1–10 (2006).
Google Scholar
Sørensen, M. E. S. et al. Comparison of independent evolutionary origins reveals both convergence and divergence in the metabolic mechanisms of symbiosis. Curr. Biol. 30, 328-334.e4 (2020).
Google Scholar
LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018).
Google Scholar
Muscatine, L. R., McCloskey, L. & Marian, E. R. Estimating the daily contribution of carbon from zooxanthellae to coral animal respiration. Limnol. Oceanogr. 26, 601–611 (1981).
Google Scholar
Anthony, K. R. N., Hoogenboom, M. O., Maynard, J. A., Grottoli, A. G. & Middlebrook, R. Energetics approach to predicting mortality risk from environmental stress: A case study of coral bleaching. Funct. Ecol. 23, 539–550 (2009).
Google Scholar
De’ath, G., Fabricius, K. E., Sweatman, H. & Puotinen, M. The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc. Natl. Acad. Sci. 109, 17995–17999 (2012).
Google Scholar
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).
Google Scholar
Davies, S. W., Marchetti, A., Ries, J. B. & Castillo, K. D. Thermal and pCO2 stress elicit divergent transcriptomic responses in a resilient coral. Front. Mar. Sci. 3, 1–15 (2016).
Google Scholar
DeSalvo, M. K., Estrada, A., Sunagawa, S. & Medina, M. Transcriptomic responses to darkness stress point to common coral bleaching mechanisms. Coral Reefs 31, 215–228 (2011).
Google Scholar
González-Pech, R. A., Vargas, S., Francis, W. R. & Wörheide, G. Transcriptomic resilience of the Montipora digitata holobiont to low pH. Front. Mar. Sci. 4, 1–9 (2017).
Google Scholar
Rubin, E. T. et al. Molecular mechanisms of coral persistence within highly urbanized locations in the Port of Miami, Florida. Front. Mar. Sci. 8, 8695236 (2021).
Google Scholar
Hawkins, T. D., Krueger, T., Wilkinson, S. P., Fisher, P. L. & Davy, S. K. Antioxidant responses to heat and light stress differ with habitat in a common reef coral. Coral Reefs 34, 1229–1241 (2015).
Google Scholar
Agostini, S., Fujimura, H., Hayashi, H. & Fujita, K. Mitochondrial electron transport activity and metabolism of experimentally bleached hermatypic corals. J. Exp. Mar. Biol. Ecol. 475, 100–107 (2016).
Google Scholar
Gardner, S. G. et al. Dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress. Proc. R. Soc. B 283, 20152418 (2016).
Google Scholar
Kenkel, C. & Matz, M. V. Gene expression plasticity as a mechanism of adaptation to a variable environment. Nat. Ecol. Evol. 1, 0014 (2016).
Google Scholar
Barshis, D. J. et al. Genomic basis for coral resilience to climate change. Proc. Natl. Acad. Sci. 110, 1387–1392 (2013).
Google Scholar
Hashimoto, K., Shibuno, T., Murayama-Kayano, E., Tanaka, H. & Kayano, T. Isolation and characterization of stress-responsive genes from the scleractinian coral Pocillopora damicornis. Coral Reefs 23, 485–491 (2004).
Rosic, N. N., Pernice, M., Dove, S., Dunn, S. & Hoegh-Guldberg, O. Gene expression profiles of cytosolic heat shock proteins Hsp70 and Hsp90 from symbiotic dinoflagellates in response to thermal stress: Possible implications for coral bleaching. Cell Stress Chaperones 16, 69–80 (2011).
Google Scholar
Meyer, E., Aglyamova, G. V. & Matz, M. V. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 20, 3599–3616 (2011).
Google Scholar
Mansour, T. A., Rosenthal, J. J. C., Brown, C. T. & Roberson, L. M. Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages. GigaScience 5, 33 (2016).
Google Scholar
Polato, N. R., Altman, N. S. & Baums, I. B. Variation in the transcriptional response of threatened coral larvae to elevated temperatures. Mol. Ecol. 22, 1366–1382 (2013).
Google Scholar
Paxton, C. W., Davy, S. K. & Weis, V. M. Stress and death of cnidarian host cells play a role in cnidarian bleaching. J. Exp. Biol. 216, 2813–2820 (2013).
Google Scholar
Matthews, J. L. et al. Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis. Proc. Natl. Acad. Sci. USA 114, 13194–13199 (2017).
Google Scholar
Jacobovitz, M. R. et al. Dinoflagellate symbionts escape vomocytosis by host cell immune suppression. Nat. Microbiol. 6, 769–782 (2021).
Google Scholar
Mitchelmore, C. L., Ringwood, A. H. & Weis, V. M. Differential accumulation of cadmium and changes in glutathione levels as a function of symbiotic state in the sea anemone Anthopleura elegantissima. J. Exp. Mar. Biol. Ecol. 284, 71–85 (2003).
Google Scholar
Dunn, S. R., Pernice, M., Green, K., Hoegh-Guldberg, O. & Dove, S. G. Thermal stress promotes host mitochondrial degradation in symbiotic cnidarians: Are the batteries of the reef going to run out?. PLoS One 7, 25 (2012).
Davy, S. K., Allemand, D. & Weis, V. M. Cell biology of cnidarian-dinoflagellate symbiosis. Microbiol. Mol. Biol. Rev. 76, 229–261 (2012).
Google Scholar
Tivey, T. R., Parkinson, J. E. & Weis, V. M. Host and symbiont cell cycle coordination is mediated by symbiotic state, nutrition, and partner identity in a model cnidarian-dinoflagellate symbiosis. MBio 11, 25 (2020).
Google Scholar
Tivey, T. R. et al. N-linked surface glycan biosynthesis, composition, inhibition, and function in cnidarian-dinoflagellate symbiosis. Mircobial Ecol. 80, 223–236 (2020).
Google Scholar
Parkinson, J. E. et al. Subtle differences in symbiont cell surface glycan profiles do not explain species-specific colonization rates in a model cnidarian-algal symbiosis. Front. Microbiol. 9, 842 (2018).
Google Scholar
Mansfield, K. M. et al. Transcription factor NF-κB is modulated by symbiotic status in a sea anemone model of cnidarian bleaching. Sci. Rep. 7, 1–14 (2017).
Google Scholar
Madin, J. S. et al. The Coral Trait Database, a curated database of trait information for coral species from the global oceans. Sci. Data 3, 160017 (2016).
Google Scholar
Dimond, J. & Carrington, E. Temporal variation in the symbiosis and growth of the temperate scleractinian coral Astrangia poculata. Mar. Ecol. Prog. Ser. 348, 161–172 (2007).
Google Scholar
Sharp, K. H., Pratte, Z. A., Kerwin, A. H., Rotjan, R. D. & Stewart, F. J. Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. Microbiome 5, 120 (2017).
Google Scholar
Dimond, J. & Carrington, E. Symbiosis regulation in a facultatively symbiotic temperate coral: Zooxanthellae division and expulsion. Coral Reefs 27, 601–604 (2008).
Google Scholar
Burmester, E. M., Finnerty, J. R., Kaufman, L. & Rotjan, R. D. Temperature and symbiosis affect lesion recovery in experimentally wounded, facultatively symbiotic temperate corals. Mar. Ecol. Prog. Ser. 570, 87–99 (2017).
Google Scholar
Wuitchik, D. M. et al. Characterizing environmental stress responses of aposymbiotic Astrangia poculata to divergent thermal challenges. Mol. Ecol. https://doi.org/10.1111/mec.16108 (2021).
Google Scholar
Schoepf, V. et al. Coral energy reserves and calcification in a high-CO2 world at two temperatures. PloS One 8, e75049 (2013).
Google Scholar
Lajeunesse, T. C., Parkinson, J. E. & Reimer, J. D. A genetics-based description of Symbiodinium minutum sp. Nov. and S. psygmophilum sp. Nov. (dinophyceae), two dinoflagellates symbiotic with cnidaria. J. Phycol. 48, 1380–1391 (2012).
Google Scholar
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Google Scholar
Li, W. & Godzik, A. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Google Scholar
Pimentel, H., Bray, N. L., Puente, S., Melsted, P. & Pachter, L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat. Methods 14, 687–690 (2017).
Google Scholar
Harrison, P. L. Sexual reproduction of scleractinian corals. In Coral Reefs: An Ecosystem in Transition (eds Dubinsky, Z. & Stambler, N.) 59–85 (Springer, 2011).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Google Scholar
Jombart, T. & Ahmed, I. adegenet 1.3–1: New tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).
Google Scholar
Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
Google Scholar
Kauffmann, A., Gentleman, R. & Huber, W. arrayQualityMetrics—a bioconductor package for quality assessment of microarray data. Bioinformatics 25, 415–416 (2009).
Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Google Scholar
Oksanen, J. et al. vegan: Community Ecology Package. (2020).
Kolde, R. pheatmap: Pretty Heatmaps. (2019).
Wright, R. M., Aglyamova, G. V., Meyer, E. & Matz, M. V. Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus. BMC Genom. 16, 1–12 (2015).
Google Scholar
Cui, G. et al. Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia. PLoS Genet. 15, 1–19 (2019).
Google Scholar
Burns, J. A., Zhang, H., Hill, E., Kim, E. & Kerney, R. Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis. Elife 6, 1–32 (2017).
Google Scholar
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016).
Google Scholar
Dixon, G. B. et al. Genomic determinants of coral heat tolerance across latitudes. Science 348, 1460–1462 (2015).
Google Scholar
Shinzato, C., Inoue, M. & Kusakabe, M. A snapshot of a coral “Holobiont”: A transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae. PLoS One 9, e85182 (2014).
Google Scholar
Maor-Landaw, K., van Oppen, M. J. H. & McFadden, G. I. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). Ecol. Evol. https://doi.org/10.1002/ece3.5910 (2019).
Google Scholar
Davies, S. W. Understanding Coral Dispersal. PhD Thesis, The University of Texas at Austin (2014).
Simona, F., Zhang, H. & Voolstra, C. R. Evidence for a role of protein phosphorylation in the maintenance of the cnidarian–algal symbiosis. Mol. Ecol. 28, 5373–5386 (2019).
Google Scholar
Xiang, T. et al. Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations. Nat. Commun. 11, 1–9 (2020).
Google Scholar
Bernard, S. M. & Habash, D. Z. The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling. New Phytol. 182, 608–620 (2009).
Google Scholar
Konishi, N. et al. Contributions of two cytosolic glutamine synthetase isozymes to ammonium assimilation in Arabidopsis roots. J. Exp. Bot. 68, 613–625 (2017).
Google Scholar
Lee, R. W., Robinson, J. J. & Cavanaugh, C. M. Pathways of inorganic nitrogen assimilation in chemoautotrophic bacteria-marine invertebrate symbioses: Expression of host and symbiont glutamine synthetase. J. Exp. Biol. 202, 289–300 (1999).
Google Scholar
Kim, D., Minhas, B. F., Li-Byarlay, H. & Hansen, A. K. Key transport and ammonia recycling genes involved in aphid symbiosis respond to host–plant specialization. Genes Genomes Genet. 8, 2433–2443 (2018).
Google Scholar
Lin, M. F., Takahashi, S., Forêt, S., Davy, S. K. & Miller, D. J. Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species. Biology Open 8, 1–11 (2019).
Su, Y., Zhou, Z. & Yu, X. Possible roles of glutamine synthetase in responding to environmental changes in a scleractinian coral. Mol. Biol. Rep. 45, 2115–2124 (2018).
Google Scholar
Hamada, M. et al. Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. Elife 7, 1–37 (2018).
Google Scholar
Hall, C. et al. Freshwater sponge hosts and their green algae symbionts: A tractable model to understand intracellular symbiosis. PeerJ 9, 1–28 (2021).
Mao, M. & Bennett, G. M. Symbiont replacements reset the co-evolutionary relationship between insects and their heritable bacteria. ISME J. 14, 1384–1395 (2020).
Google Scholar
Fam, R. R. S. et al. Molecular characterization of a novel algal glutamine synthetase (GS) and an algal glutamate synthase (GOGAT) from the colorful outer mantle of the giant clam, Tridacna squamosa, and the putative GS-GOGAT cycle in its symbiotic zooxanthellae. Gene 656, 40–52 (2018).
Google Scholar
Gates, R. D., Hoegh-Guldberg, O., McFall-Ngai, M. J., Bil, K. Y. & Muscatine, L. Free amino acids exhibit anthozoan “host factor” activity: They induce the release of photosynthate from symbiotic dinoflagellates in vitro. Proc. Natl. Acad. Sci. 92, 7430–7434 (1995).
Google Scholar
Perland, E., Bagchi, S., Klaesson, A. & Fredriksson, R. Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: Evolutionary conservation, predicted structure and neuronal co-expression. Open Biol. 7, 25 (2017).
Google Scholar
Kenkel, C. D., Meyer, E. & Matz, M. V. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol. Ecol. 22, 4322–4334 (2013).
Google Scholar
Yuyama, I., Ishikawa, M., Nozawa, M., Yoshida, M. & Ikeo, K. Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis. Sci. Rep. 8, 1–11 (2018).
Google Scholar
Rodriguez-Lanetty, M., Phillips, W. S. & Weis, V. M. Transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression. BMC Genom. 7, 1–11 (2006).
Google Scholar
Xu, X. et al. Specific structure and unique function define the hemicentin. Cell Biosci. 3, 27 (2013).
Google Scholar
Smith, T. E. & Moran, N. A. Coordination of host and symbiont gene expression reveals a metabolic tug-of-war between aphids and Buchnera. Proc. Natl. Acad. Sci. USA 117, 2113–2121 (2020).
Google Scholar
Sun, Y. et al. Signaling pathway of MAPK/ERK in cell proliferation, differentiation, migration, senescence and apoptosis. J. Recept. Signal Transduct. 35, 600–604 (2015).
Google Scholar
Lisovsky, M., Itoh, K. & Sokol, S. Y. Frizzled receptors activate a novel JNK-dependent pathway that may lead to apoptosis. Curr. Biol. 12, 53–58 (2002).
Google Scholar
Jiang, X. & Wang, X. Cytochrome c-mediated apoptosis. Annu. Rev. Biochem. 73, 87–106 (2004).
Google Scholar
Detournay, O. & Weis, V. M. Role of the sphingosine rheostat in the regulation of cnidarian-dinoflagellate symbioses. Biol. Bull. 221, 261–269 (2011).
Google Scholar
Wolfowicz, I. et al. Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians. Sci. Rep. 6, 1–12 (2016).
Google Scholar
Weis, V. M. Cell biology of coral symbiosis: Foundational study can inform solutions to the coral reef crisis. Integr. Comp. Biol. 59, 845–855 (2019).
Google Scholar
Mansfield, K. M. et al. Varied effects of algal symbionts on transcription factor NF-kB in a sea anemone and a coral: Possible roles in symbiosis and thermotolerance. bioRxiv 5444, 25 (2019).
Zuliani-Alvarez, L. et al. Mapping tenascin-C interaction with toll-like receptor 4 reveals a new subset of endogenous inflammatory triggers. Nat. Commun. 8, 25 (2017).
Google Scholar
Piccinini, A. M. & Midwood, K. S. Endogenous control of immunity against infection: Tenascin-C regulates TLR4-mediated inflammation via microRNA-155. Cell Rep. 2, 914–926 (2012).
Google Scholar
Thompson, J. R., Rivera, H. E., Closek, C. J. & Medina, M. Microbes in the coral holobiont: Partners through evolution, development, and ecological interactions. Front. Cell. Infect. Microbiol. 4, 1–20 (2014).
Maynard, J. et al. Projections of climate conditions that increase coral disease susceptibility and pathogen abundance and virulence. Nat. Clim. Change 5, 688–694 (2015).
Google Scholar
Alvarez-Filip, L., Estrada-Saldívar, N., Pérez-Cervantes, E., Molina-Hernández, A. & González-Barrios, F. J. A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 2019, 25 (2019).
Walton, C. J., Hayes, N. K. & Gilliam, D. S. Impacts of a regional, multi-year, multi-species coral disease outbreak in Southeast Florida. Front. Mar. Sci. 5, 1–14 (2018).
Google Scholar
Weil, E., Hernández-Delgado, E. A., Gonzalez, M., Williams, S. & Figuerola, M. Spread of the new coral disease “SCTLD” into the Caribbean: Implications for Puerto Rico. Reef Encounter 34, 38–43 (2019).
Rippe, J. P., Kriefall, N. G., Davies, S. W. & Castillo, K. D. Differential disease incidence and mortality of inner and outer reef corals of the upper Florida Keys in association with a white syndrome outbreak. Bull. Mar. Sci. 95, 305–316 (2019).
Google Scholar
DeFilippo, L., Burmester, E. M., Kaufman, L. & Rotjan, R. D. Patterns of surface lesion recovery in the Northern Star Coral, Astrangia poculata. J. Exp. Mar. Biol. Ecol. 481, 15–24 (2016).
Google Scholar
Leydet, K. P. & Hellberg, M. E. The invasive coral Oculina patagonica has not been recently introduced to the Mediterranean from the western Atlantic. BMC Evol. Biol. 15, 79 (2015).
Google Scholar
Leydet, K. P. & Hellberg, M. E. Discordant coral–symbiont structuring: Factors shaping geographical variation of Symbiodinium communities in a facultative zooxanthellate coral genus, Oculina. Coral Reefs 35, 583–595 (2016).
Google Scholar
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