Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora

Influence of sipunculan (peanut worm) activity on orifice formation in scleractinian Heterocyathus for adaptation to soft substrates

Mutualism profoundly affects the morphology and ecological evolution of both hosts and symbionts involved. Heterocyathus is a solitary scleractinian coral that lives on soft substrata, and sipunculan worms live symbiotically in the tube-like cavities (orifice) inside the coral skeletons. This habitat provides protection to the sipunculan worms against predators and-owing to the mobility of the worms-prevents the coral from being buried with sediments. The orifice growth is closely related to the symbiont sipunculan worms; however, this has not been previously elucidated. Here, we clarified the growth process of scleractinian coral orifices and the influence of sipunculan activity on this. The orifices were originally formed by rapid accretion deposits. The coral soft tissue enveloping the growth edge of the orifice repeatedly retreated to the outer side due to direct damage to the soft part and/or excessive stress caused by the rubbing of the sipunculan through locomotion, excretion, and feeding behaviour. This resulted in a toppled-domino microskeletal structure appearance and maintenance of the orifice growth. These outcomes demonstrate the first example of the direct influence of symbionts on the skeletal morphogenesis of scleractinian corals. The mutualism between the two organisms is maintained by the beneficial confrontation in forming orifices.

The Matrix Protein Cysrichin, a Galaxin-like Protein from Hyriopsis cumingii, Induces Vaterite Formation In Vitro

In this study, we cloned a novel matrix protein, cysrichin, with 16.03% homology and a similar protein structure to the coral biomineralized protein galaxin. Tissue expression analysis showed that cysrichin was mainly expressed in mantle and gill tissues. In situ hybridization indicated that cysrichin mRNA was detected in the entire epithelium region of mantle tissue. RNAi analysis and shell notching experiment confirmed that cysrichin participates in the prismatic layer and nacreous layer formation of the shell. An in vitro crystallization experiment showed that the cysrichin protein induced lotus-shaped and round-shaped crystals, which were identified as vaterite crystals. These results may provide new clues for understanding the formation of vaterite in freshwater shellfish.

Wound healing and regeneration in the reef building coral Acropora millepora

Branching scleractinian corals are niche-constructing organisms, providing continuously-growing, structural foundation for spectacularly biodiverse coral reef ecosystems. A large part of their success lies in the ability to quickly regenerate following mechanical damage. Even now, when the corals undergo great decline due to anthropogenic weather and storm extremes, it is surprising how little is known about molecular mechanisms governing regeneration in these iconic organisms. In this study, we used RNA-seq to identify genes involved in the regeneration of Acropora millepora, starting with the initial wound closure up to complete rebuilding of lost structures. Many of the differentially expressed genes we found in the wound healing steps are homologues of genes known to be involved in wound healing and regeneration of bilaterian and other cnidarian species, prominently including multiple components of FGF and Wnt signalling pathways. Comparison between genes involved in wound healing and continuous growth of the colony demonstrates both similarity and distinctiveness of the genetic programmes controlling these processes. A striking example is specific expression of c-Fos, a transcription factor with conserved role in early injury response, during the earliest stages of wound healing of A. millepora. By comparing results obtained in diverse experimental conditions including a closed-loop, recirculating aquarium and a flow-through system of marine station, we have demonstrated feasibility of using zooxanthellate scleractinian corals as experimental models in fundamental biology research, including studies of regeneration.

Different skeletal protein toolkits achieve similar structure and performance in the tropical coral Stylophora pistillata and the temperate Oculina patagonica

Stony corals (order: Scleractinia) differ in growth form and structure. While stony corals have gained the ability to form their aragonite skeleton once in their evolution, the suite of proteins involved in skeletogenesis is different for different coral species. This led to the conclusion that the organic portion of their skeleton can undergo rapid evolutionary changes by independently evolving new biomineralization-related proteins. Here, we used liquid chromatography-tandem mass spectrometry to sequence skeletogenic proteins extracted from the encrusting temperate coral Oculina patagonica. We compare it to the previously published skeletal proteome of the branching subtropical corals Stylophora pistillata as both are regarded as highly resilient to environmental changes. We further characterized the skeletal organic matrix (OM) composition of both taxa and tested their effects on the mineral formation using a series of overgrowth experiments on calcite seeds. We found that each species utilizes a different set of proteins containing different amino acid compositions and achieve a different morphology modification capacity on calcite overgrowth. Our results further support the hypothesis that the different coral taxa utilize a species-specific protein set comprised of independent gene co-option to construct their own unique organic matrix framework. While the protein set differs between species, the specific predicted roles of the whole set appear to underline similar functional roles. They include assisting in forming the extracellular matrix, nucleation of the mineral and cell signaling. Nevertheless, the different composition might be the reason for the varying organization of the mineral growth in the presence of a particular skeletal OM, ultimately forming their distinct morphologies.

Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp

In hermatypic scleractinian corals, photosynthetic fixation of CO2 and the production of CaCO3 are intimately linked due to their symbiotic relationship with dinoflagellates of the Symbiodiniaceae family. This makes it difficult to study ion transport mechanisms involved in the different pathways. In contrast, most ahermatypic scleractinian corals do not share this symbiotic relationship and thus offer an advantage when studying the ion transport mechanisms involved in the calcification process. Despite this advantage, non-symbiotic scleractinian corals have been systematically neglected in calcification studies, resulting in a lack of data especially at the molecular level. Here, we combined a tissue micro-dissection technique and RNA-sequencing to identify calcification-related ion transporters, and other candidates, in the ahermatypic non-symbiotic scleractinian coral Tubastraea spp. Our results show that Tubastraea spp. possesses several calcification-related candidates previously identified in symbiotic scleractinian corals (such as SLC4-γ, AMT-1like, CARP, etc.). Furthermore, we identify and describe a role in scleractinian calcification for several ion transporter candidates (such as SLC13, -16, -23, etc.) identified for the first time in this study. Taken together, our results provide not only insights about the molecular mechanisms underlying non-symbiotic scleractinian calcification, but also valuable tools for the development of biotechnological solutions to better control the extreme invasiveness of corals belonging to this particular genus.

Gene expression alterations from reversible to irreversible stages during coral metamorphosis

For corals, metamorphosis from planktonic larvae to sedentary polyps is an important life event, as it determines the environment in which they live for a lifetime. Although previous studies on the reef-building coral Acropora have clarified a critical time point during metamorphosis when cells are committed to their fates, as defined by an inability to revert back to their previous states as swimming larvae (here referred to as the "point of no return"), the molecular mechanisms of this commitment to a fate remain unclear. To address this issue, we analyzed the transcriptomic changes before and after the point of no return by inducing metamorphosis of Acropora tenuis with Hym-248, a metamorphosis-inducing neuropeptide. Gene Ontology and pathway enrichment analysis of the 5893 differentially expressed genes revealed that G protein-coupled receptors (GPCRs) were enriched, including GABA receptor and Frizzled gene subfamilies, which showed characteristic temporal expression patterns. The GPCRs were then classified by comparison with those of Homo sapiens, Nematostella vectensis and Platynereis dumerilii. Classification of the differentially expressed genes into modules based on expression patterns showed that some modules with large fluctuations after the point of no return were biased toward functions such as protein metabolism and transport. This result suggests that in precommitted larvae, different types of GPCR genes function to ensure a proper environment, whereas in committed larvae, intracellular protein transport and proteolysis may cause a loss of the reversibility of metamorphosis as a result of cell differentiation.

Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification

Corals are the ecosystem engineers of coral reefs, one of the most biodiverse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO₃) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for example, whether corals employ different molecular machineries to deposit different CaCO₃ polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.

The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

Background

The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals.

Results

We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution.

Conclusion

Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.

How corals made rocks through the ages

Hard, or stony, corals make rocks that can, on geological time scales, lead to the formation of massive reefs in shallow tropical and subtropical seas. In both historical and contemporary oceans, reef-building corals retain information about the marine environment in their skeletons, which is an organic-inorganic composite material. The elemental and isotopic composition of their skeletons is frequently used to reconstruct the environmental history of Earth's oceans over time, including temperature, pH, and salinity. Interpretation of this information requires knowledge of how the organisms formed their skeletons. The basic mechanism of formation of calcium carbonate skeleton in stony corals has been studied for decades. While some researchers consider coral skeletons as mainly passive recorders of ocean conditions, it has become increasingly clear that biological processes play key roles in the biomineralization mechanism. Understanding the role of the animal in living stony coral biomineralization and how it evolved has profound implications for interpreting environmental signatures in fossil corals to understand past ocean conditions. Here we review historical hypotheses and discuss the present understanding of how corals evolved and how their skeletons changed over geological time. We specifically explain how biological processes, particularly those occurring at the subcellular level, critically control the formation of calcium carbonate structures. We examine the different models that address the current debate including the tissue-skeleton interface, skeletal organic matrix, and biomineralization pathways. Finally, we consider how understanding the biological control of coral biomineralization is critical to informing future models of coral vulnerability to inevitable global change, particularly increasing ocean acidification.

New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes

A general trend observed in animal skeletomes-the proteins occluded in animal skeletons-is the copresence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend. However, distributions and phylogenetic analyses of biomineralization-related genes are often based on only a few species, with other anthozoan calcifiers such as octocorals (soft corals), not being fully considered. We de novo assembled the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs. calcitic sclerites) and data-mined published nonbilaterian transcriptome resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. Cnidaria shared no skeletome proteins with Placozoa or Ctenophora, but did share some skeletome proteins with Porifera, such as galaxin-related proteins. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes such as secreted acidic proteins, scleritin, and carbonic anhydrases, and propose an early, single biomineralization-recruitment event for galaxin sensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion into the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e., aragonite/calcite) with no differences in the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins such as galaxins and SCRiP-3a could represent instances of commonality.

Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides

The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.

Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions

Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO₃.

Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification

Recent studies have indicated that various corals might have different degrees of resistance to elevated CO₂ levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO₂ levels. The calcification rates were higher in high CO₂ treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca²⁺ transporters were present in the calcium signaling pathway, which could be important in the CO₂ regulation of coral calcification. The gene expression levels of many CO₂ and HCO₃^- transporters were not affected by elevated CO₂. Nevertheless, high CO₂ levels did have an effect on the expression of certain Ca²⁺ transporters. The upregulation of Ca²⁺ transporters likely explained the higher resistance of A. austera to high CO₂ than A. cerealis.

Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions

Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO₃.

Elevated CO2 delays the early development of scleractinian coral Acropora gemmifera

The effects of elevated CO₂ on the early life stages of coral were investigated by culturing the pelagic larvae and new recruits of Acropora gemmifera at three concentrations of CO₂ (corresponding to pH = 8.1, 7.8 and 7.5, respectively). Acidified seawater resulted in fewer A. gemmifera larvae settling, and led to the production of smaller new recruits by slowing the development of the skeleton. The delayed development of new recruits due to elevated CO₂ was consistent with the downregulation of calcification related genes. Several genes related to HCO₃^- and Ca²⁺ transporters were downregulated by elevated CO₂, with solute carriers (SLC) (membrane transport proteins) possibly playing an important role. The downregulation of these membrane transport proteins might suppress the transport of calcium, bicarbonate and organic matter, resulting in the delayed development of A. gemmifera.

Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral

BACKGROUND

Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization.

RESULTS

Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are "primed" for settlement. Rise of competence through development was accompanied by up-regulation of sensory and signal transduction genes such as ion channels, genes involved in neuropeptide signaling, and G-protein coupled receptor (GPCRs). A drug screen targeting components of GPCR signaling pathways confirmed a role in larval settlement behavior and metamorphosis.

CONCLUSIONS

These results gives insight into the molecular complexity underlying these transitions and reveals receptors and pathways that, if altered by changing environments, could affect dispersal capabilities of reef-building corals. In addition, this dataset provides a toolkit for asking broad questions about sensory capacity in multicellular animals and the evolution of development.

Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals)

Corallimorpharians (coral-like anemones) have a close phylogenetic relationship with scleractinians (hard corals) and can potentially provide novel perspectives on the evolution of biomineralization within the anthozoan subclass Hexacorallia. A survey of the transcriptomes of three representative corallimorpharians led to the identification of homologs of some skeletal organic matrix proteins (SOMPs) previously considered to be restricted to corals.

Carbonic anhydrases (CAs), which are ubiquitous proteins involved in CO₂ trafficking, are involved in both coral calcification and photosynthesis by endosymbiotic Symbiodinium (zooxanthellae). These multiple roles are assumed to place increased demands on the CA repertoire and have presumably driven the elaboration of the complex CA repertoires typical of corals (note that “corals” are defined here as reef-building Scleractinia). Comparison of the CA inventories of corallimorpharians with those of corals reveals that corals have specifically expanded the secreted and membrane-associated type CAs, whereas similar complexity is observed in the two groups with respect to other CA types.

Comparison of the CA complement of the nonsymbiotic corallimorph Corynactis australis with that of Ricordea yuma, a corallimorph which normally hosts Symbiodinium, reveals similar numbers and distribution of CA types and suggests that an expansion of the CA repertoire has been necessary to enable calcification but may not be a requirement to enable symbiosis. Consistent with this idea, preliminary analysis suggests that the CA complexity of zooxanthellate and nonzooxanthellate sea anemones is similar.

The comparisons above suggest that although there are relatively few new genes in the skeletal organic matrix of corals (which controls the skeleton deposition process), the evolution of calcification required an expanded repertoire of secreted and membrane-associated CAs.

Identifying genes and regulatory pathways associated with the scleractinian coral calcification process

Reef building corals precipitate calcium carbonate as an exo-skeleton and provide substratum for prosperous marine life. Biomineralization of the coral’s skeleton is a developmental process that occurs concurrently with other proliferation processes that control the animal extension and growth. The development of the animal body is regulated by large gene regulatory networks, which control the expression of gene sets that progressively generate developmental patterns in the animal body. In this study we have explored the gene expression profile and signaling pathways followed by the calcification process of a basal metazoan, the Red Sea scleractinian (stony) coral, Stylophora pistillata. When treated by seawater with high calcium concentrations (addition of 100 gm/L, added as CaCl₂.2H₂O), the coral increases its calcification rates and associated genes were up-regulated as a result, which were then identified. Gene expression was compared between corals treated with elevated and normal calcium concentrations. Calcification rate measurements and gene expression analysis by microarray RNA transcriptional profiling at two time-points (midday and night-time) revealed several genes common within mammalian gene regulatory networks. This study indicates that core genes of the Wnt and TGF-β/BMP signaling pathways may also play roles in development, growth, and biomineralization in early-diverging organisms such as corals.

Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners

In the South China Sea, coastal eutrophication in the Beibu Gulf has seriously threatened reef habitats by subjecting corals to chronic physiological stress. To determine how coral holobionts may tolerate such conditions, we examined the transcriptomes of healthy colonies of the galaxy coral Galaxea fascicularis and its endosymbiont Symbiodinium from two reef sites experiencing pristine or eutrophied nutrient regimes. We identified 236 and 205 genes that were differentially expressed in eutrophied hosts and symbionts, respectively. Both gene sets included pathways related to stress responses and metabolic interactions. An analysis of genes originating from each partner revealed striking metabolic integration with respect to vitamins, cofactors, amino acids, fatty acids, and secondary metabolite biosynthesis. The expression levels of these genes supported the existence of a continuum of mutualism in this coral-algal symbiosis. Additionally, large sets of transcription factors, cell signal transduction molecules, biomineralization components, and galaxin-related proteins were expanded in G. fascicularis relative to other coral species.

Temporal and spatial expression patterns of biomineralization proteins during early development in the stony coral Pocillopora damicornis

Reef-building corals begin as non-calcifying larvae that, upon settling, rapidly begin to accrete skeleton and a protein-rich skeletal organic matrix that attach them to the reef. Here, we characterized the temporal and spatial expression pattern of a suite of biomineralization genes during three stages of larval development in the reef-building coral Pocillopora damicornis: stage I, newly released; stage II, oral-aborally compressed and stage III, settled and calcifying spat. Transcriptome analysis revealed 3882 differentially expressed genes that clustered into four distinctly different patterns of expression change across the three developmental stages. Immunolocalization analysis further reveals the spatial arrangement of coral acid-rich proteins (CARPs) in the overall architecture of the emerging skeleton. These results provide the first analysis of the timing of the biomineralization 'toolkit' in the early life history of a stony coral.

Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics

Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteome of the scleractinian coral, Acropora digitifera, for which large genomic and transcriptomic datasets are available. Scrupulous gene annotation was conducted based on comparisons of functional domain structures among metazoans. We found that SOMPs include not only coral-specific proteins, but also protein families that are widely conserved among cnidarians and other metazoans. We also identified several conserved transmembrane proteins in the skeletal proteome. Gene expression analysis revealed that expression of these conserved genes continues throughout development. Therefore, these genes are involved not only skeleton formation, but also in basic cellular functions, such as cell-cell interaction and signaling. On the other hand, genes encoding coral-specific proteins, including extracellular matrix domain-containing proteins, galaxins, and acidic proteins, were prominently expressed in post-settlement stages, indicating their role in skeleton formation. Taken together, the process of coral skeleton formation is hypothesized as: 1) formation of initial extracellular matrix between epithelial cells and substrate, employing pre-existing transmembrane proteins; 2) additional extracellular matrix formation using novel proteins that have emerged by domain shuffling and rapid molecular evolution and; 3) calcification controlled by coral-specific SOMPs.

Comparative genomics explains the evolutionary success of reef-forming corals

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals under environmental stress. Some of these genes arose through horizontal gene transfer and comprise at least 0.2% of the animal gene inventory. Our analysis elucidates the evolutionary strategies that have allowed symbiotic corals to adapt and thrive for hundreds of millions of years.

DOI:http://dx.doi.org/10.7554/eLife.13288.001

For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals.

Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so.

The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity.

Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer.

The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions.

DOI:http://dx.doi.org/10.7554/eLife.13288.002

Recent advances in genomics and transcriptomics of cnidarians

The advent of the genomic era has provided important and surprising insights into the deducted genetic composition of the common ancestor of cnidarians and bilaterians. This has changed our view of how genomes of metazoans evolve and when crucial gene families arose and diverged in animal evolution. Sequencing of several cnidarian genomes showed that cnidarians share a great part of their gene repertoire as well as genome synteny with vertebrates, with less gene losses in the anthozoan cnidarian lineage than for example in ecdysozoans like Drosophila melanogaster or Caenorhabditis elegans. The Hydra genome on the other hand has evolved more rapidly indicated by more divergent sequences, more cases of gene losses and many taxonomically restricted genes. Cnidarian genomes also contain a rich repertoire of transcription factors, including those that in bilaterian model organisms regulate the development of key bilaterian traits such as mesoderm, nervous system development and bilaterality. The sea anemone Nematostella vectensis, and possibly cnidarians in general, does not only share its complex gene repertoire with bilaterians, but also the regulation of crucial developmental regulatory genes via distal enhancer elements. In addition, epigenetic modifications on DNA and chromatin are shared among eumetazoans. This suggests that most conserved genes present in our genomes today, as well as the mechanisms guiding their expression, evolved before the divergence of cnidarians and bilaterians about 600 Myr ago.

Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals

The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.

The genetics of colony form and function in Caribbean Acropora corals

Background

Colonial reef-building corals have evolved a broad spectrum of colony morphologies based on coordinated asexual reproduction of polyps on a secreted calcium carbonate skeleton. Though cnidarians have been shown to possess and use similar developmental genes to bilaterians during larval development and polyp formation, little is known about genetic regulation of colony morphology in hard corals. We used RNA-seq to evaluate transcriptomic differences between functionally distinct regions of the coral (apical branch tips and branch bases) in two species of Caribbean Acropora, the staghorn coral, A. cervicornis, and the elkhorn coral, A. palmata.

Results

Transcriptome-wide gene profiles differed significantly between different parts of the coral colony as well as between species. Genes showing differential expression between branch tips and bases were involved in developmental signaling pathways, such as Wnt, Notch, and BMP, as well as pH regulation, ion transport, extracellular matrix production and other processes. Differences both within colonies and between species identify a relatively small number of genes that may contribute to the distinct “staghorn” versus “elkhorn” morphologies of these two sister species.

Conclusions

The large number of differentially expressed genes supports a strong division of labor between coral branch tips and branch bases. Genes involved in growth of mature Acropora colonies include the classical signaling pathways associated with development of cnidarian larvae and polyps as well as morphological determination in higher metazoans.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1133) contains supplementary material, which is available to authorized users.

Gene discovery in the finger leather coral Sinularia notanda by construction and sequencing of a normalized cDNA library

The transplantation of coral fragments is one of methods that restore coral communities. To form coral colonies, the fragmented corals initiated skeletal extension from the cut-edge of fragment then success the settlement. In order to understand the molecular events underlying fragment adhesion and settlement, we constructed a normalized cDNA library and generated and annotated expressed sequence tags (ESTs) from the fragmented adult polyps of soft coral Sinularia notanda. We generated 3251 high-quality ESTs with an average length of 580 bp and the EST cluster and assembly analyses produced 2796 unigenes, including 2487 singletons and 309 contigs. Of the known genes, 55 genes were sel ected to be involved in polyp fragment adhesion and settlement based on Gene Ontology (GO) classification. Notably, two EST clones were identified to show homology with galaxin gene which was demonstrated as coral specific calcifying protein of organic matrix. These EST sequences can provide utility as molecular markers in molecular and genetic studies of S. notanda and other soft coral.

Shaping the microenvironment: evidence for the influence of a host galaxin on symbiont acquisition and maintenance in the squid-Vibrio symbiosis

Most bacterial species make transitions between habitats, such as switching from free living to symbiotic niches. We provide evidence that a galaxin protein, EsGal1, of the squid Euprymna scolopes participates in both: (i) selection of the specific partner Vibrio fischeri from the bacterioplankton during symbiosis onset and, (ii) modulation of V. fischeri growth in symbiotic maintenance. We identified two galaxins in transcriptomic databases and showed by quantitative reverse-transcriptase polymerase chain reaction that one (esgal1) was dominant in the light organ. Further, esgal1 expression was upregulated by symbiosis, a response that was partially achieved with exposure to symbiont cell-envelope molecules. Confocal immunocytochemistry of juvenile animals localized EsGal1 to the apical surfaces of light-organ epithelia and surrounding mucus, the environment in which V. fischeri cells aggregate before migration into the organ. Growth assays revealed that one repeat of EsGal1 arrested growth of Gram-positive bacterial cells, which represent the cell type first 'winnowed' during initial selection of the symbiont. The EsGal1-derived peptide also significantly decreased the growth rate of V. fischeri in culture. Further, when animals were exposed to an anti-EsGal1 antibody, symbiont population growth was significantly increased. These data provide a window into how hosts select symbionts from a rich environment and govern their growth in symbiosis.

Molecular evolution of calcification genes in morphologically similar but phylogenetically unrelated scleractinian corals

Molecular phylogenies of scleractinian corals often fail to agree with traditional phylogenies derived from morphological characters. These discrepancies are generally attributed to non-homologous or morphologically plastic characters used in taxonomic descriptions. Consequently, morphological convergence of coral skeletons among phylogenetically unrelated groups is considered to be the major evolutionary process confounding molecular and morphological hypotheses. A strategy that may help identify cases of convergence and/or diversification in coral morphology is to compare phylogenies of existing "neutral" genetic markers used to estimate genealogic phylogenetic history with phylogenies generated from non-neutral genes involved in calcification (biomineralization). We tested the hypothesis that differences among calcification gene phylogenies with respect to the "neutral" trees may represent convergent or divergent functional strategies among calcification gene proteins that may correlate to aspects of coral skeletal morphology. Partial sequences of two nuclear genes previously determined to be involved in the calcification process in corals, "Cnidaria-III" membrane-bound/secreted α-carbonic anhydrase (CIII-MBSα-CA) and bone morphogenic protein (BMP) 2/4, were PCR-amplified, cloned and sequenced from 31 scleractinian coral species in 26 genera and 9 families. For comparison, "neutral" gene phylogenies were generated from sequences from two protein-coding "non-calcification" genes, one nuclear (β-tubulin) and one mitochondrial (cytochrome b), from the same individuals. Cloned CIII-MBSα-CA sequences were found to be non-neutral, and phylogenetic analyses revealed CIII-MBSα-CAs to exhibit a complex evolutionary history with clones distributed between at least 2 putative gene copies. However, for several coral taxa only one gene copy was recovered. With CIII-MBSα-CA, several recovered clades grouped taxa that differed from the "non-calcification" loci. In some cases, these taxa shared aspects of their skeletal morphology (i.e., convergence or diversification relative to the "non-calcification" loci), but in other cases they did not. For example, the "non-calcification" loci recovered Atlantic and Pacific mussids as separate evolutionary lineages, whereas with CIII-MBSα-CA, clones of two species of Atlantic mussids (Isophyllia sinuosa and Mycetophyllia sp.) and two species of Pacific mussids (Acanthastrea echinata and Lobophyllia hemprichii) were united in a distinct clade (except for one individual of Mycetophyllia). However, this clade also contained other taxa which were not unambiguously correlated with morphological features. BMP2/4 also contained clones that likely represent different gene copies. However, many of the sequences showed no significant deviation from neutrality, and reconstructed phylogenies were similar to the "non-calcification" tree topologies with a few exceptions. Although individual calcification genes are unlikely to precisely explain the diverse morphological features exhibited by scleractinian corals, this study demonstrates an approach for identifying cases where morphological taxonomy may have been misled by convergent and/or divergent molecular evolutionary processes in corals. Studies such as this may help illuminate our understanding of the likely complex evolution of genes involved in the calcification process, and enhance our knowledge of the natural history and biodiversity within this central ecological group.

Gene expression patterns during the early stages of chemically induced larval metamorphosis and settlement of the coral Acropora millepora

The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement.

Transcriptome analysis of the scleractinian coral Stylophora pistillata

The principal architects of coral reefs are the scleractinian corals; these species are divided in two major clades referred to as “robust” and “complex” corals. Although the molecular diversity of the “complex” clade has received considerable attention, with several expressed sequence tag (EST) libraries and a complete genome sequence having been constructed, the “robust” corals have received far less attention, despite the fact that robust corals have been prominent focal points for ecological and physiological studies. Filling this gap affords important opportunities to extend these studies and to improve our understanding of the differences between the two major clades. Here, we present an EST library from Stylophora pistillata (Esper 1797) and systematically analyze the assembled transcripts compared to putative homologs from the complete proteomes of six well-characterized metazoans: Nematostella vectensis, Hydra magnipapillata, Caenorhabditis elegans, Drosophila melanogaster, Strongylocentrotus purpuratus, Ciona intestinalis and Homo sapiens. Furthermore, comparative analyses of the Stylophora pistillata ESTs were performed against several Cnidaria from the Scleractinia, Actiniaria and Hydrozoa, as well as against other stony corals separately. Functional characterization of S. pistillata transcripts into KOG/COG categories and further description of Wnt and bone morphogenetic protein (BMP) signaling pathways showed that the assembled EST library provides sufficient data and coverage. These features of this new library suggest considerable opportunities for extending our understanding of the molecular and physiological behavior of “robust” corals.

The molecular mechanism of calcification in aquatic organisms

Biomineralization is a process of mineral deposition by organisms. Calcium salts are the major component of various biominerals, calcium carbonate being the predominant type in aquatic organisms. The mechanism of biomineralization has been conventionally analyzed by microscopic observation. The findings obtained suggest that minute amounts of organic matrices in biominerals play a key role in biomineralization. We first introduced the methodology of bioactive compound chemistry into this research field. Using various biominerals, such as the exoskeleton and gastroliths of the crayfish, the otoliths and scales of fish, the coccoliths of coccolithophores, bivalve shells, and coral skeleton, a range of organic matrices were purified by simple functional assays, and their chemical structures were determined. The function of each matrix component was estimated by its ability to interact with calcium carbonate and by in vitro crystallization, immunological localization, and site-specific and temporal expression of the encoding genes in the case of proteins and peptides, among other compounds. It was found that there was almost no similarity in chemical structure among organic matrices from various biominerals, but similarity in function was observed, and that made possible the functional classification of organic matrices.

The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling

In corals, biocalcification is a major function that may be drastically affected by ocean acidification (OA). Scleractinian corals grow by building up aragonitic exoskeletons that provide support and protection for soft tissues. Although this process has been extensively studied, the molecular basis of biocalcification is poorly understood. Notably lacking is a comprehensive catalog of the skeleton-occluded proteins—the skeletal organic matrix proteins (SOMPs) that are thought to regulate the mineral deposition. Using a combination of proteomics and transcriptomics, we report the first survey of such proteins in the staghorn coral Acropora millepora. The organic matrix (OM) extracted from the coral skeleton was analyzed by mass spectrometry and bioinformatics, enabling the identification of 36 SOMPs. These results provide novel insights into the molecular basis of coral calcification and the macroevolution of metazoan calcifying systems, whereas establishing a platform for studying the impact of OA at molecular level. Besides secreted proteins, extracellular regions of transmembrane proteins are also present, suggesting a close control of aragonite deposition by the calicoblastic epithelium. In addition to the expected SOMPs (Asp/Glu-rich, galaxins), the skeletal repertoire included several proteins containing known extracellular matrix domains. From an evolutionary perspective, the number of coral-specific proteins is low, many SOMPs having counterparts in the noncalcifying cnidarians. Extending the comparison with the skeletal OM proteomes of other metazoans allowed the identification of a pool of functional domains shared between phyla. These data suggest that co-option and domain shuffling may be general mechanisms by which the trait of calcification has evolved.

Scleractinian coral cell proliferation is reduced in primary culture of suspended multicellular aggregates compared to polyps

Cell cultures from reef-building scleractinian corals are being developed to study the response of these ecologically important organisms to environmental stress and diseases. Despite the importance of cell division to support propagation, cell proliferation in polyps and in vitro is under-investigated. In this study, suspended multicellular aggregates (tissue balls) were obtained after collagenase dissociation of Pocillopora damicornis coral, with varying yields between enzyme types and brands. Ultrastructure and cell type distribution were characterized in the tissue balls (TBs) compared to the polyp. Morphological evidence of cellular metabolic activity in their ciliated cortex and autophagy in their central mass suggests involvement of active tissue reorganization processes. DNA synthesis was evaluated in the forming multicellular aggregates and in the four cell layers of the polyp, using BrdU labeling of nuclei over a 24 h period. The distribution of BrdU-labeled coral cells was spatially heterogeneous and their proportion was very low in tissue balls (0.2 ± 0.1 %), indicating that suspended multicellular aggregate formation does not involve significant cell division. In polyps, DNA synthesis was significantly lower in the calicoderm (<1 %) compared to both oral and aboral gastroderm (about 10 %) and to the pseudostratified oral epithelium (15-25 % at tip of tentacle). DNA synthesis in the endosymbiotic dinoflagellates dropped in the forming tissue balls (2.7 ± 1.2 %) compared to the polyp (14 ± 3.4 %) where it was not different from the host gastroderm (10.3 ± 1.2 %). A transient (24 h) increase was observed in the cell-specific density of dinoflagellates in individually dissociated coral cell cultures. These results suggest disruption of coral cell proliferation processes upon establishment in primary culture.

Gene expression signatures of energetic acclimatisation in the reef building coral Acropora millepora

BACKGROUND

Understanding the mechanisms by which natural populations cope with environmental stress is paramount to predict their persistence in the face of escalating anthropogenic impacts. Reef-building corals are increasingly exposed to local and global stressors that alter nutritional status causing reduced fitness and mortality, however, these responses can vary considerably across species and populations.

METHODOLOGY/PRINCIPAL FINDINGS

We compare the expression of 22 coral host genes in individuals from an inshore and an offshore reef location using quantitative Reverse Transcription-PCR (qRT-PCR) over the course of 26 days following translocation into a shaded, filtered seawater environment. Declines in lipid content and PSII activity of the algal endosymbionts (Symbiodinium ITS-1 type C2) over the course of the experiment indicated that heterotrophic uptake and photosynthesis were limited, creating nutritional deprivation conditions. Regulation of coral host genes involved in metabolism, CO2 transport and oxidative stress could be detected already after five days, whereas PSII activity took twice as long to respond. Opposing expression trajectories of Tgl, which releases fatty acids from the triacylglycerol storage, and Dgat1, which catalyses the formation of triglycerides, indicate that the decline in lipid content can be attributed, at least in part, by mobilisation of triacylglycerol stores. Corals from the inshore location had initially higher lipid content and showed consistently elevated expression levels of two genes involved in metabolism (aldehyde dehydrogenase) and calcification (carbonic anhydrase).

CONCLUSIONS/SIGNIFICANCE

Coral host gene expression adjusts rapidly upon change in nutritional conditions, and therefore can serve as an early signature of imminent coral stress. Consistent gene expression differences between populations indicate that corals acclimatize and/or adapt to local environments. Our results set the stage for analysis of these processes in natural coral populations, to better understand the responses of coral communities to global climate change and to develop more efficient management strategies.

Genes related to ion-transport and energy production are upregulated in response to CO2-driven pH decrease in corals: new insights from transcriptome analysis

Since the preindustrial era, the average surface ocean pH has declined by 0.1 pH units and is predicted to decline by an additional 0.3 units by the year 2100. Although subtle, this decreasing pH has profound effects on the seawater saturation state of carbonate minerals and is thus predicted to impact on calcifying organisms. Among these are the scleractinian corals, which are the main builders of tropical coral reefs. Several recent studies have evaluated the physiological impact of low pH, particularly in relation to coral growth and calcification. However, very few studies have focused on the impact of low pH at the global molecular level. In this context we investigated global transcriptomic modifications in a scleractinian coral (Pocillopora damicornis) exposed to pH 7.4 compared to pH 8.1 during a 3-week period. The RNAseq approach shows that 16% of our transcriptome was affected by the treatment with 6% of upregulations and 10% of downregulations. A more detailed analysis suggests that the downregulations are less coordinated than the upregulations and allowed the identification of several biological functions of interest. In order to better understand the links between these functions and the pH, transcript abundance of 48 candidate genes was quantified by q-RT-PCR (corals exposed at pH 7.2 and 7.8 for 3 weeks). The combined results of these two approaches suggest that pH≥7.4 induces an upregulation of genes coding for proteins involved in calcium and carbonate transport, conversion of CO2 into HCO3(-) and organic matrix that may sustain calcification. Concomitantly, genes coding for heterotrophic and autotrophic related proteins are upregulated. This can reflect that low pH may increase the coral energy requirements, leading to an increase of energetic metabolism with the mobilization of energy reserves. In addition, the uncoordinated downregulations measured can reflect a general trade-off mechanism that may enable energy reallocation.

Genotype - environment correlations in corals from the Great Barrier Reef

Background

Knowledge of genetic markers that are correlated to stress tolerance may improve spatial mapping of reef vulnerability and can inform restoration efforts, including the choice of genotypes for breeding and reseeding. In this manuscript we present two methods for screening transcriptome data for candidate genetic markers in two reef building corals, Acropora millepora and Pocillopora damicornis (types α and β). In A. millepora, Single Nucleotide Polymorphisms (SNPs) were pre-selected by targeting genes believed to be involved in the coral thermal stress responses. In P. damicornis (type α and β), SNPs showing varying allele frequencies between two populations from distinct environments were pre-selected. Allele frequencies at nine, five and eight of the pre-selected SNP loci were correlated against gradients of water clarity and temperature in a large number of populations along the Great Barrier Reef.

Results

A significant correlation between environmental category and SNP allele frequency was detected in up to 55% of the tested loci, which is an exceptional success rate for these types of tests. In P. damicornis, SNP allele frequencies of β-hexosaminidase and Elongation factor 1-α were significantly correlated to temperature in type α and to temperature and/or water clarity respectively in type β. Type α also showed a correlation between water clarity and SNP allele frequency in a gene of unknown function. In A. millepora, allele frequencies at five (β-gamma crystallin, Galaxin, Ubiquitin, Ligand of Numb X2 and Thioredoxin) SNP loci showed significant correlations.

Conclusions

After validation of these candidate loci through laboratory or field assessment of relative stress tolerance of colonies harbouring different alleles, it is anticipated that a proportion of these markers may represent the first coral candidate Quantitative Trait Loci for environmental stress tolerance and provide an important genetic tool that can be incorporated into spatial management decisions and restoration efforts of coral reefs. One pertinent example would be to combine spatial data of tolerant populations with genetic connectivity and thus identify high priority conservation reefs and implement targeted coral husbandry and active restoration efforts that use locally- and stress-adapted genotypes.

Cell biology of cnidarian-dinoflagellate symbiosis

The symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genus Symbiodinium is of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidarian-dinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between green Hydra and its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future.

Using bacterial extract along with differential gene expression in Acropora millepora larvae to decouple the processes of attachment and metamorphosis

Biofilms of the bacterium Pseudoalteromonas induce metamorphosis of acroporid coral larvae. The bacterial metabolite tetrabromopyrrole (TBP), isolated from an extract of Pseudoalteromonas sp. associated with the crustose coralline alga (CCA) Neogoniolithon fosliei, induced coral larval metamorphosis (100%) with little or no attachment (0–2%). To better understand the molecular events and mechanisms underpinning the induction of Acropora millepora larval metamorphosis, including cell proliferation, apoptosis, differentiation, migration, adhesion and biomineralisation, two novel coral gene expression assays were implemented. These involved the use of reverse-transcriptase quantitative PCR (RT-qPCR) and employed 47 genes of interest (GOI), selected based on putative roles in the processes of settlement and metamorphosis. Substantial differences in transcriptomic responses of GOI were detected following incubation of A. millepora larvae with a threshold concentration and 10-fold elevated concentration of TBP-containing extracts of Pseudoalteromonas sp. The notable and relatively abrupt changes of the larval body structure during metamorphosis correlated, at the molecular level, with significant differences (p<0.05) in gene expression profiles of 24 GOI, 12 hours post exposure. Fourteen of those GOI also presented differences in expression (p<0.05) following exposure to the threshold concentration of bacterial TBP-containing extract. The specificity of the bacterial TBP-containing extract to induce the metamorphic stage in A. millepora larvae without attachment, using a robust, low cost, accurate, ecologically relevant and highly reproducible RT-qPCR assay, allowed partially decoupling of the transcriptomic processes of attachment and metamorphosis. The bacterial TBP-containing extract provided a unique opportunity to monitor the regulation of genes exclusively involved in the process of metamorphosis, contrasting previous gene expression studies that utilized cues, such as crustose coralline algae, biofilms or with GLW-amide neuropeptides that stimulate the entire onset of larval metamorphosis and attachment.

Differential gene expression at coral settlement and metamorphosis--a subtractive hybridization study

Background

A successful metamorphosis from a planktonic larva to a settled polyp, which under favorable conditions will establish a future colony, is critical for the survival of corals. However, in contrast to the situation in other animals, e.g., frogs and insects, little is known about the molecular basis of coral metamorphosis. We have begun to redress this situation with previous microarray studies, but there is still a great deal to learn. In the present paper we have utilized a different technology, subtractive hybridization, to characterize genes differentially expressed across this developmental transition and to compare the success of this method to microarray.

Methodology/Principal Findings

Suppressive subtractive hybridization (SSH) was used to identify two pools of transcripts from the coral, Acropora millepora. One is enriched for transcripts expressed at higher levels at the pre-settlement stage, and the other for transcripts expressed at higher levels at the post-settlement stage. Virtual northern blots were used to demonstrate the efficacy of the subtractive hybridization technique. Both pools contain transcripts coding for proteins in various functional classes but transcriptional regulatory proteins were represented more frequently in the post-settlement pool. Approximately 18% of the transcripts showed no significant similarity to any other sequence on the public databases. Transcripts of particular interest were further characterized by in situ hybridization, which showed that many are regulated spatially as well as temporally. Notably, many transcripts exhibit axially restricted expression patterns that correlate with the pool from which they were isolated. Several transcripts are expressed in patterns consistent with a role in calcification.

Conclusions

We have characterized over 200 transcripts that are differentially expressed between the planula larva and post-settlement polyp of the coral, Acropora millepora. Sequence, putative function, and in some cases temporal and spatial expression are reported.

²⁶Mg labeling of the sea urchin regenerating spine: Insights into echinoderm biomineralization process

This paper reports the results of the first dynamic labeling experiment with regenerating spines of sea urchins Paracentrotus lividus using the stable isotope ²⁶Mg and NanoSIMS high-resolution isotopic imaging, which provide a direct information about the growth process. Growing spines were labeled twice (for 72 and 24 h, respectively) by increasing the abundance of ²⁶Mg in seawater. The incorporation of ²⁶Mg into the growing spines was subsequently imaged with the NanoSIMS ion microprobe. Stereom trabeculae initially grow as conical micro-spines, which form within less than 1 day. These micro-spines fuse together by lateral outgrowths and form a thin, open meshwork (inner stereom), which is subsequently reinforced by addition of layered thickening deposits (outer stereom). The (longitudinal) growth rate of the inner stereom is ca. 125 μm/day. A single (ca. 1 μm) thickening layer in the stereom trabeculae is deposited during 24h. The thickening process is contemporaneous with the formation micro-spines and involves both longitudinal trabeculae and transverse bridges to a similar degree. Furthermore, the skeleton-forming cells remain active in the previously formed open stereom for at least 10 days, and do not migrate upwards until the end of the thickening process. The experimental capability presented here provides a new way to obtain detailed information about the skeleton formation of a multitude of marine, calcite producing organisms.

A unique skeletal microstructure of the deep-sea micrabaciid scleractinian corals

Micrabaciids are solitary, exclusively azooxanthellate deep-sea corals belonging to one of the deepest-living (up to 5,000 m) scleractinian representatives. All modern micrabaciid taxa (genera: Letepsammia, Rhombopsammia, Stephanophyllia, Leptopenus) have a porous and often very fragile skeleton consisting of two main microstructural components known also from other scleractinians: rapid accretion deposits and thickening deposits. However, at the microstructural level, the skeletal organization of the micrabaciids is distinctly different from that of other scleractinians. Rapid accretion deposits consist of alternations of superimposed "microcrystalline" (micrometer-sized aggregates of nodular nanodomains) and fibrous zones. In contrast to all shallow-water and sympatric deep-water corals so far described, the thickening deposits of micrabaciids are composed of irregular meshwork of short (1-2 μm) and extremely thin (ca. 100-300 nm) fibers organized into small, chip-like bundles (ca. 1-2 μm thick). Longer axes of fiber bundles are usually subparallel to the skeletal surfaces and oriented variably in this plane. The unique microstructural organization of the micrabaciid skeleton is consistent with their monophyletic status based on macromorphological and molecular data, and points to a diversity of organic matrix-mediated biomineralization strategies in Scleractinia.

New tricks with old genes: the genetic bases of novel cnidarian traits

Recent thought on genome evolution has focused on the creation of new genes and changes in regulatory mechanisms while ignoring the role of selective gene loss in shaping genomes. Using data from two cnidarians, the jellyfish Clytia and the coral Acropora, we examined the relative significance of new 'taxonomically restricted' genes and selectively retained ancestral genes in enabling the evolution of novel traits. Consistent with its more complex life-cycle, the proportion of novel genes identified in Clytia was higher than that in the 'polyp only' cnidarians Nematostella and Hydra, but each of these cnidarians has retained a proportion of ancestral genes not present in the other two. The ubiquity and near-stochastic nature of gene loss can explain the discord between patterns of gene distribution and taxonomy.