Development and heat stress-induced transcriptomic changes during embryogenesis of the coral Acropora palmata
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ABSTRACT:
ORGANISM(S): Acropora palmata
SUBMITTER: Kevin Portune
PROVIDER: E-GEOD-21038 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Projected elevation of seawater temperatures poses a threat to the reproductive success of Caribbean reef-building corals that have planktonic development during the warmest months of the year. This study examined the transcriptomic changes that occurred during embryonic and larval development of the elkhorn coral, Acropora palmata, at a non-stressful temperature (28°C) and further assessed the effects of two elevated temperatures (30°C and 31.5°C) on these expression patterns. Using cDNA microarrays, we compared expression levels of 2,051 genes from early embryos and larvae at multiple developmental stages (including pre-blastula, blastula, gastrula, and planula stages) at each of the three temperatures. At 12 hours post-fertilization in 28°C treatments, genes involved in cell replication/cell division and transcription were up-regulated in A. palmata embryos, followed by a reduction in expression of these genes during later growth stages. From 24.5 to 131 hours post-fertilization at 28°C, A. palmata altered its transcriptome by up-regulating genes involved in protein synthesis and metabolism. Temperatures of 30°C and 31.5°C caused major changes to the A. palmata embryonic transcriptomes, particularly in the samples from 24.5 hpf post-fertilization, characterized by down-regulation of numerous genes involved in cell replication/cell division, metabolism, cytoskeleton, and transcription, while heat shock genes were up-regulated compared to 28°C treatments. These results suggest that increased temperature may cause a breakdown in proper gene expression during development in A. palmata by down-regulation of genes involved in essential cellular processes, which may lead to the abnormal development and reduced survivorship documented in other studies.
2010-03-25 | GSE21038 | GEO
Project description:Background Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5C, 29.0C, and 31.5C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours. Results Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the long-term regulation upon heat stress. Conclusions Embryos responded differently depending on exposure time and temperature level. Embryos showed expression of stress-related genes already at a temperature of 29.0C, but seemed to be able to counteract the initial response over time. By contrast, embryos at 31.5C displayed continuous expression of stress genes. The genes that played a role in the response to elevated temperatures consisted of both highly conserved and coral-specific genes. These genes might serve as a basis for research into coral-specific adaptations to stress responses and global climate change. The experimental setup followed a reference design, i.e. all samples were hybridized against the same pool made up of equal amounts of RNA from all samples. We used three technical replicates for each temperature. Common reference samples were labeled with Cy3, temperature samples with Cy5. Microarrays for M. faveolata contained 1,314 coding sequences, of which 43% had functional annotations as determined by homology to known genes.
2010-05-06 | E-GEOD-15088 | biostudies-arrayexpress
Project description:Coral reefs are based on the symbiotic relationship between corals and photosynthetic dinoflagellates of the genus Symbiodinium. We followed gene expression of coral larvae of Acropora palmata and Montastraea faveolata after exposure to Symbiodinium strains that differed in their ability to establish symbioses. We show that the coral host transcriptome remains almost unchanged during infection by competent symbionts, but is massively altered by symbionts that fail to establish symbioses. Our data suggest that successful coral-algal symbioses depend mainly on the symbionts' ability to enter the host in a stealth manner rather than a more active response from the coral host. Acropora palmata Samples: Three biological replicates of pooled larvae from each species and condition (i.e. untreated control, inoculated with competent Symbiodinium strain, inoculated with incompetent Symbiodinium strain) for both time points were hybridized against a pooled reference. Pooled references were constructed by combining equal amounts of aRNA from all control samples from A. palmata. References were labeled with Cy3, samples with Cy5. Montastraea faveolata Samples: Three biological replicates of pooled larvae from each species and condition (i.e. untreated control, inoculated with competent Symbiodinium strain, inoculated with incompetent Symbiodinium strain) for both time points were hybridized against a pooled reference. Pooled references were constructed by combining equal amounts of aRNA from all control samples from M. faveolata. References were labeled with Cy3, samples with Cy5. Symbiodinium sp. CassKB8: competent strain Symbiodinium sp. EL1: incompetent strain Symbiodinium sp. Mf1.05b: competent strain
2010-06-20 | E-GEOD-14923 | biostudies-arrayexpress
Project description:The emergence of genomic tools for reef-building corals and symbiotic anemones comes at a time when alarming losses in coral cover are being observed worldwide. These tools hold great promise in elucidating novel and unforeseen cellular processes underlying the successful mutualism between corals and their algal endosymbionts (Symbiodinium spp.). Since thermal stress triggers a breakdown in the symbiosis (coral bleaching), measuring the transcriptomic response to thermal stress-induced bleaching offers an extraordinary view of the cellular processes specific to coral-algal symbioses. In the present study, we utilized a cDNA microarray containing 2,059 genes of the Caribbean Elkhorn coral Acropora palmata to identify genes differentially expressed upon thermal stress. Fragments from four separate colonies were exposed to elevated temperature (3ËC increase) for two days, and samples were frozen for microarray analysis after 24 and 48 hours. Fragments experienced a 60% reduction in algal cell density after two days. 204 genes were differentially expressed in samples collected one day after thermal stress; in samples collected after two days, 104 genes. Annotations of the differentially expressed genes indicate a conserved cellular stress response in A. palmata involving: 1) growth arrest; 2) chaperone activity; 3) nucleic acid stabilization and repair; and 4) the removal of damaged macromolecules. Other differentially expressed processes include sensory perception, metabolite transfer between host and symbiont, nitric oxide signaling, and modifications to the actin cytoskeleton and extracellular matrix. The results are also compared to those from a previous coral microarray study of thermal stress in Montastraea faveolata. The field experiment was performed at the Smithsonian Tropical Research Instituteâs Bocas del Toro field station in Panamá during September and October 2006. Four colonies of A. palmata were sampled from two separate reefs 21 km apart (two colonies from Isla Solarte â 9o19â56.78â N and 82o12â54.65â W, and two colonies from Cayos Zapatillas â 9o15â08.79â N and 82o02â24.63â W). Each colony was broken into six fragments using a hammer and chisel. For each colony, three fragments were placed in a control aquarium, and three fragments were placed in an experimental aquarium fitted with two 200-Watt aquarium heaters, such that each colony was represented by a pair of aquaria (total of three control and three heated aquaria, all 75-liter). The three control aquaria were placed in one large fiberglass pond with continuous water flow, and the three experimental aquaria were placed in another large pond. All aquaria were exposed to shaded ambient light, and each aquarium was a closed system (but contained a pump to generate continuous water flow). Fragments were kept at a depth of ~25cm. HOBO Pendant Temperature/Light Data Loggers (Onset Corp UA-002-64) recorded temperature and light data every three minutes. These data loggers are not designed to measure photosynthetically active radiation (PAR â 400-700nm), as only ~30% of the measured light is in the range of PAR. For this reason, relative light levels in the aquaria are reported (expressed as the percentage of the average 10am to 2pm light intensity measured on a reef ~4m deep in Bocas del Toro (9o22â68.4â N and 82o18â24.6â W) during September and October 2007). Light intensity differed slightly between the four aquaria fitted with HOBOs (control aquaria 1 â 43%; control aquaria 2 â 46%; heated aquaria 1 â 35%; and heated aquaria 2 â 34% of reef light). After an acclimation period of four days at the natural temperature of the seawater system (mean temperature = 30.29±0.07oC), a fragment from each control and experimental aquaria was sampled (t0C and t0H). After time zero sampling, the heaters in each of the experimental aquaria were turned on. The temperatures of the experimental aquaria increased to ca. 32oC over three hours. The mean temperature of the control aquaria during the entire experiment was 29.74±0.03oC, and the mean temperature of the heated aquaria was 32.72±0.32oC. Control and experimental fragments were sampled again one day (1dC and 1dH) and two days (2dC and 2dH) after turning on the heaters. Heated fragments from one of the colonies (col3) showed extreme bleaching after one day of thermal stress. The remaining fragment of col3 was removed at this time to avoid fouling of the water due to death. Thus, there are four replicates for t0C, t0H, 1dC, and 1dH, and three replicates for 2dC and 2dH. All samples were taken at night. Fragments were frozen in liquid nitrogen. We employed a reference design where all control and heat-stressed samples were compared to a pooled reference aRNA sample composed of aRNA from the four t0C fragments. Since all RNA samples were compared to the reference sample, direct comparisons of gene expression across all time points and conditions can be performed.
2010-06-20 | E-GEOD-16151 | biostudies-arrayexpress
Project description:Coral bleaching occurs in response to numerous abiotic stressors, the ecologically most relevant of which is hyperthermic stress due to increasing seawater temperatures. Bleaching events can span large geographic areas and are currently a potent threat to coral reefs worldwide. Much effort has been focused on understanding the molecular and cellular events underlying bleaching, and these studies have mainly utilized heat and light stress regimes. In an effort to determine whether different stressors share common bleaching mechanisms, we used cDNA microarrays for the corals Acropora palmata and Montastraea faveolata (containing > 10,000 features) to measure differential gene expression during darkness stress. This is the first coral microarray experiment aimed at darkness stress, and the first for these species to interrogate gene expression at such a large scale. Our results reveal a striking transcriptomic response to darkness in A. palmata involving chaperone and antioxidant up-regulation, growth arrest, and metabolic modifications. As these responses were also measured during thermal stress, our results suggest that different stressors may share common bleaching mechanisms. Furthermore, our results point to ER stress as a critical cellular event involved in darkness-specific (and possibly more general) molecular bleaching mechanisms. On the other hand, we identified a meager transcriptomic response to darkness in M. faveolata where gene expression differences between host colonies and/or sampling locations were greater than differences between control and stressed fragments. To this end, we discuss the importance of factors related to host genotype, Symbiodinium genotype, and the abiotic environment that influence host gene expression and thereby can hinder an investigator’s ability to measure gene expression during a condition of interest. We employed a reference design where all control and dark-stressed samples were compared to a pooled reference aRNA sample composed of aRNA from all fragments. Since all RNA samples were compared to the reference sample, direct comparisons of gene expression across all time points and conditions can be performed.
2011-03-22 | E-GEOD-27024 | biostudies-arrayexpress
Project description:Coral bleaching occurs in response to numerous abiotic stressors, the ecologically most relevant of which is hyperthermic stress due to increasing seawater temperatures. Bleaching events can span large geographic areas and are currently a potent threat to coral reefs worldwide. Much effort has been focused on understanding the molecular and cellular events underlying bleaching, and these studies have mainly utilized heat and light stress regimes. In an effort to determine whether different stressors share common bleaching mechanisms, we used cDNA microarrays for the corals Acropora palmata and Montastraea faveolata (containing > 10,000 features) to measure differential gene expression during darkness stress. This is the first coral microarray experiment aimed at darkness stress, and the first for these species to interrogate gene expression at such a large scale. Our results reveal a striking transcriptomic response to darkness in A. palmata involving chaperone and antioxidant up-regulation, growth arrest, and metabolic modifications. As these responses were also measured during thermal stress, our results suggest that different stressors may share common bleaching mechanisms. Furthermore, our results point to ER stress as a critical cellular event involved in darkness-specific (and possibly more general) molecular bleaching mechanisms. On the other hand, we identified a meager transcriptomic response to darkness in M. faveolata, where gene expression differences between host colonies and/or sampling locations were greater than differences between control and stressed fragments. To this end, we discuss the importance of factors related to host genotype, Symbiodinium genotype, and the abiotic environment that influence host gene expression and thereby can hinder an investigator’s ability to measure gene expression during a condition of interest. We employed a reference design where all control and dark-stressed samples were compared to a pooled reference aRNA sample composed of aRNA from all fragments. Since all RNA samples were compared to the reference sample, direct comparisons of gene expression across all time points and conditions can be performed.
2011-03-22 | E-GEOD-27022 | biostudies-arrayexpress
Project description:Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects. Hybridization followed a dual channel loop design using two biological replicates (dye-swapped) from each treatment that maximized power to detect differential expression in contrasts between temperatures and batches (within time-points) as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 18 arrays on two 12 plex slides were used (Table S1). Additional samples from other sub-batches (b3/b4) were included in the microarray experiment but are not used in this analysis. Each array measures the expression level of 135,185 genes from the elkhorn coral (Acropora palmata) transcriptome (Polato et al. 2011). Two 60-mer probes were designed for each contig (n = 85,260), and a single probe was designed for each singleton sequence (n = 45,390). Two additional probes each were developed for sequences associated with annotation information relating to calcium metabolism and stress response (n = 4,798). Replicate probes for individual sequences from the assembled transcriptome were not identical; rather they represented multiple different 60-mer sequences from the original template.
2012-12-13 | E-GEOD-36983 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE27022: Microarray studies of darkness stress and bleaching in the Caribbean coral Acropora palmata GSE27024: Microarray studies of darkness stress and bleaching in the Caribbean coral Montastraea faveolata Refer to individual Series
2011-03-22 | E-GEOD-27025 | biostudies-arrayexpress
Project description:Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies. Microarray experiments were performed as follows. Appropriate Cy3 and Cy5 labeled DNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES and 3 × SSC, resulting in a final volume of 70?l. The hybridization mixtures were boiled for 2 min at 99°C and allowed to cool at room temperature for 5 min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 55°C. Microarrays were washed once in 2 × SSC, 0.03% SDS heated to 55 °C for 5 min. followed by one wash in 1 x SSC and another wash in 0.2 x SSC for 5 min each. The slides were kept in 0.2 × SSC until analysis. Slides were dried via centrifugation and scanned using an Axon 4000B scanner. The experimental setup followed a reference design, i.e., all samples were hybridized against the same pool of labeled A. palmata DNA. For each species, a total of four hybridizations were performed, including two dye swap hybridizations in order to account for potential dye bias i.e. two hybridizations with Cy3 labeled M. faveolata DNA against a Cy5 labeled A. palmata reference and two hybridizations with Cy5 labeled M. faveolata DNA against a Cy3 labeled Cy3 A. palmata reference were performed. The same hybridization scheme was used for A. cervicornis and S. radians.
2012-11-22 | E-GEOD-37279 | biostudies-arrayexpress
Project description:Several microorganisms have wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments. To better understand thermal adaptation of psychrotrophs, Exiguobacterium sibiricum strain 255-15 was used, a psychrotrophic bacterium that grows from -5°C to 39°C. Its genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 CDS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 10°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response. Keywords: stress response to cold and hot temperatures Six-condition experiment: -2.5°C vs10°C, -2.5°C vs 28°C, -2.5°C vs 39°C, 28°C vs10°C, 28°C vs 39°C, 10°C vs 39°C. Biological replicates: 6 replicates grown and harvested independently for each different temperature (-2.5°C, 10°C, 28°C and 39°C). One replicate per array.
2010-05-26 | E-GEOD-10133 | biostudies-arrayexpress