Rinkevich B. Will two walk together, except they have agreed? Amos 3: 3. J Evol Biol. 2004;17:1178–9.
CAS PubMed Article Google Scholar
Rinkevich B. Quo vadis chimerism? Chimerism. 2011;2:1–5.
PubMed PubMed Central Article Google Scholar
Rinkevich B. Coral chimerism as an evolutionary rescue mechanism to mitigate global climate change impacts. Glob Chang Biol. 2019;25:1198–206.
Article Google Scholar
Maier E, Buckenmaier A, Tollrian R, Nürnberger B. Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix. Coral Reefs. 2012;31:505–17.
Article Google Scholar
Puill-Stephan E, Willis B, Abrego D, Raina J-B, van Oppen M. Allorecognition maturation in the broadcast-spawning coral Acropora millepora. Coral Reefs. 2012;31:1019–28.
Article Google Scholar
Rinkevich B, Shaish L, Douek J, Ben-Shlomo R. Venturing in coral larval chimerism: a compact functional domain with fostered genotypic diversity. Sci Rep. 2016;6:19493.
CAS PubMed PubMed Central Article Google Scholar
Schweinsberg M, Weiss LC, Striewski S, Tollrian R, Lampert KP. More than one genotype: how common is intracolonial genetic variability in scleractinian corals? Mol Ecol. 2015;24:2673–85.
PubMed Article Google Scholar
Amar K-O, Chadwick NE, Rinkevich B. Coral kin aggregations exhibit mixed allogeneic reactions and enhanced fitness during early ontogeny. BMC Ecol Evol. 2008;8:126.
Google Scholar
Amar K-O, Rinkevich B. Mounting of erratic histoincompatible responses in hermatypic corals: a multi-year interval comparison. J Exp Biol. 2010;213:535–40.
PubMed Article Google Scholar
Barki Y, Gateño D, Graur D, Rinkevich B. Soft-coral natural chimerism: a window in ontogeny allows the creation of entities comprised of incongruous parts. Mar Ecol Prog Ser. 2002;231:91–9.
Article Google Scholar
Frank U, Oren U, Loya Y, Rinkevich B. Alloimmune maturation in the coral Stylophora pistillata is achieved through three distinctive stages, 4 months post–metamorphosis. Proc Biol Sci. 1997;264:99–104.
PubMed Central Article Google Scholar
Jiang L, Lei X-M, Liu S, Huang H. Fused embryos and pre-metamorphic conjoined larvae in a broadcast spawning reef coral. F1000Research. 2015;4:44.
Mizrahi D, Navarrete SA, Flores AA. Groups travel further: pelagic metamorphosis and polyp clustering allow higher dispersal potential in sun coral propagules. Coral Reefs. 2014;33:443–8.
Article Google Scholar
Rinkevich B, Yankelevich I. Environmental split between germ cell parasitism and somatic cell synergism in chimeras of a colonial urochordate. J Exp Biol. 2004;207:3531–6.
PubMed Article Google Scholar
Eirin-Lopez JM, Putnam HM. Marine environmental epigenetics. Annu Rev Mar Sci. 2019;11:335–68.
Article Google Scholar
Torda G, Donelson JM, Aranda M, Barshis DJ, Bay L, Berumen ML, et al. Rapid adaptive responses to climate change in corals. Nat Clim Chang. 2017;7:627.
Article Google Scholar
Rivera HE, Aichelman HE, Fifer JE, Kriefall NG, Wuitchik DM, Wuitchik SJS, et al. A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol Ecol. 2021;30:1381–97.
CAS PubMed Article Google Scholar
Barshis DJ, Ladner JT, Oliver TA, Seneca FO, Traylor-Knowles N, Palumbi SR. Genomic basis for coral resilience to climate change. Proc Natl Acad Sci U S A. 2013;110:1387–92.
CAS PubMed PubMed Central Article Google Scholar
Kenkel CD, Matz MV. Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nat Ecol Evol. 2016;1:0014.
Article Google Scholar
Brener-Raffalli K, Vidal-Dupiol J, Adjeroud M, Rey O, Romans P, Bonhomme F, et al. Gene expression plasticity and frontloading promote thermotolerance in Pocillopora corals. Peer Commun J. 2022;2:e13.
Bay RA, Palumbi SR. Transcriptome predictors of coral survival and growth in a highly variable environment. Ecol Evol. 2017;7:4794–803.
PubMed PubMed Central Article Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–D6.
PubMed PubMed Central Article CAS Google Scholar
Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot J-F, et al. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. Sci Rep. 2017;7:17583.
PubMed PubMed Central Article CAS Google Scholar
Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, et al. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep. 2016;6:39734.
CAS PubMed PubMed Central Article Google Scholar
Grösch S, Alessenko AV, Albi E. The many facets of sphingolipids in the specific phases of acute inflammatory response. Mediat Inflamm. 2018;2018:5378284.
Article CAS Google Scholar
Whitacre JM. Biological robustness: paradigms, mechanisms, and systems principles. Front Genet. 2012;3:67.
PubMed PubMed Central Google Scholar
Huffmyer AS, Drury C, Majerová E, Lemus JD, Gates RD. Tissue fusion and enhanced genotypic diversity support the survival of Pocillopora acuta coral recruits under thermal stress. Coral Reefs. 2021;40:447–58.
Article Google Scholar
Shefy D, Shashar N, Rinkevich B. Exploring traits of engineered coral entities to be employed in reef restoration. J Mar Sci Eng. 2020;8:1038.
Article Google Scholar
Rinkevich B. Human natural chimerism: an acquired character or a vestige of evolution? Hum Immunol. 2001;62:651–7.
CAS PubMed Article Google Scholar
Stoner DS, Rinkevich B, Weissman IL. Heritable germ and somatic cell lineage competitions in chimeric colonial protochordates. Proc Natl Acad Sci U S A. 1999;96:9148–53.
CAS PubMed PubMed Central Article Google Scholar
Bosch TCG. Cnidarian-microbe interactions and the origin of innate immunity in metazoans. Annu Rev Microbiol. 2013;67:499–518.
CAS PubMed Article Google Scholar
Hay ED. Cell biology of extracellular matrix: Springer Science & Business Media; 2013.
Google Scholar
McClintock B. The significance of responses of the genome to challenge. Science. 1984;226:792–801.
CAS PubMed Article Google Scholar
Bellantuono AJ, Dougan KE, Granados-Cifuentes C, Rodriguez-Lanetty M. Transcriptome landscape of a thermal-tolerant coral endosymbiont reveals molecular signatures of symbiosis and dysbiosis (2019). Preprint at //doi.org/10.1101/508184.
Maor-Landaw K, van Oppen MJH, McFadden GI. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). Ecol Evol. 2020;10:451–66.
PubMed Article Google Scholar
Fifer J, Bentlage B, Lemer S, Fujimura AG, Sweet M, Raymundo LJ. Going with the flow: how corals in high-flow environments can beat the heat. Mol Ecol. 2021;30:2009–24.
CAS PubMed Article Google Scholar
Desalvo MK, Sunagawa S, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M. Coral host transcriptomic states are correlated with Symbiodinium genotypes. Mol Ecol. 2010;19:1174–86.
CAS PubMed Article Google Scholar
Barshis DJ, Ladner JT, Oliver TA, Palumbi SR. Lineage-specific transcriptional profiles of Symbiodinium spp. unaltered by heat stress in a coral host. Mol Biol Evol. 2014;31:1343–52.
CAS PubMed Article Google Scholar
Gierz SL, Forêt S, Leggat W. Transcriptomic analysis of thermally stressed Symbiodinium reveals differential expression of stress and metabolism genes. Front Plant Sci. 2017;8.
Bates AE, Cooke RS, Duncan MI, Edgar GJ, Bruno JF, Benedetti-Cecchi L, et al. Climate resilience in marine protected areas and the ‘Protection Paradox’. Biol Conserv. 2019;236:305–14.
Article Google Scholar
Bruno JF, Côté IM, Toth LT. Climate change, coral loss, and the curious case of the parrotfish paradigm: why don’t marine protected areas improve reef resilience? Annu Rev Mar Sci. 2019;11:307–34.
Article Google Scholar
Rinkevich B. Management of coral reefs: we have gone wrong when neglecting active reef restoration. Mar Pollut Bull. 2008;56:1821–4.
CAS PubMed Article Google Scholar
Horoszowski-Fridman YB, Brêthes J-C, Rahmani N, Rinkevich B. Marine silviculture: incorporating ecosystem engineering properties into reef restoration acts. Ecol Eng. 2015;82:201–13.
Article Google Scholar
Raymundo LJ, Maypa AP. Getting bigger faster: mediation of size-specific mortality via fusion in juvenile coral transplants. Ecol Appl. 2004;14:281–95.
Article Google Scholar
Rinkevich B. The active reef restoration toolbox is a vehicle for coral resilience and adaptation in a changing world. J Mar Sci Eng. 2019;7:201.
Article Google Scholar
Shefy D, Shashar N, Rinkevich B. The reproduction of the Red Sea coral Stylophora pistillata from Eilat: 4-decade perspective. Mar Biol. 2018;165:27.
Article Google Scholar
R: A language and environment for statistical computing. R Foundation for Statistical Computing (2021). //www.R-project.org/. Accessed 11 Aug 2021.
Siebeck U, Marshall N, Klüter A, Hoegh-Guldberg O. Monitoring coral bleaching using a colour reference card. Coral Reefs. 2006;25:453–60.
Article Google Scholar
Banguera-Hinestroza E, Saenz-Agudelo P, Bayer T, Berumen ML, Voolstra CR. Characterization of new microsatellite loci for population genetic studies in the Smooth Cauliflower Coral (Stylophora sp.). Conserv Genet Resour. 2013;5:561–3.
Article Google Scholar
Krueger F. Trim galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files; 2015.
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
CAS PubMed Article Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
PubMed PubMed Central Article CAS Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing (2012). Preprint at //doi.org/10.48550/arXiv.1207.390.
Vidal-Dupiol J, Harscouet E, Shefy D, Toulza E, Rey O, Alienne J-F, et al. Transcriptome and composition of chimeric and non-chimeric coral holobiont of the species Stylophora pistillata in response to translocation. IFREMER. 2020. //doi.org/10.12770/86ff6c42-3771-45eb-9164-a18159d7c7fe.
Vidal-Dupiol J, Harscouet E, Shefy D, Toulza E, Rey O, Alienne J-F et al. Transcriptome and composition of chimeric and non-chimeric coral holobiont of the species Stylophora pistillata in response to translocation. NCBI. 2022. //www.ncbi.nlm.nih.gov/sra/PRJNA858201.
Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge: Babraham Bioinformatics, Babraham Institute; 2010.
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
CAS PubMed Article Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biol. 2014;15:550.
Dixon G, Liao Y, Bay LK, Matz MV. Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc Natl Acad Sci U S A. 2018;115:13342–6.
CAS PubMed PubMed Central Article Google Scholar
Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24:1403–5.
CAS PubMed Article Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1-e.
Article CAS Google Scholar
LaJeunesse T, Trench R. Biogeography of two species of Symbiodinium (Freudenthal) inhabiting the intertidal sea anemone Anthopleura elegantissima (Brandt). Biol Bull. 2000;199:126–34.
CAS PubMed Article Google Scholar
Quigley KM, Davies SW, Kenkel CD, Willis BL, Matz MV, Bay LK. Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals. PLoS One. 2014;9:e94297.
PubMed PubMed Central Article CAS Google Scholar
Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, et al. FROGS: find, rapidly, OTUs with galaxy solution. Bioinformatics. 2017;34:1287–94.
Article CAS Google Scholar
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
PubMed PubMed Central Article CAS Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17:10–2.
Article Google Scholar
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ. 2014;2:e593.
PubMed PubMed Central Article Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
PubMed PubMed Central Article Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
CAS PubMed Article Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8:e61217.
CAS PubMed PubMed Central Article Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289–300.
Google Scholar
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Chimeras display higher survival in natura. (A) S. pistillata chimeras (A1) following fusion between two genetically different spats that are still distinguishable; (A2) a 1-year-old juvenile chimera resulting from the fusion of two genetically different spats. Both partners are intermingled and form a single colony with the same morphology as non-chimeras. (B) Survival of non-chimeras (unicolor coral) and chimeras (bi-color coral) over 6 and 12 months of exposure to regular and natural environmental conditions at 10-m depth assessed at the 95% confidence intervals using the “Cloper – Pearson” method and chi-square. (C) Translocation experiment, from 10 to 2m, used to induce an abrupt environmental change characterized by higher temperature variation (CV. coefficient of variation) and average light intensity (μ in lux)