Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1119670 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29282457_1.fastq.gz | Fastqsanger.gz | |||
| SRR29282457_2.fastq.gz | Fastqsanger.gz | |||
| SRR29282458_1.fastq.gz | Fastqsanger.gz | |||
| SRR29282458_2.fastq.gz | Fastqsanger.gz | |||
| SRR29282459_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:A mutualistic relationship between reef-building corals and endosymbiotic algae (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. If, and to what extent, differences in algal symbiont clade contents can exert effects on the coral host transcriptome is currently unknown. In this study, we monitored algal physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered coral fragments using a custom cDNA gene expression microarray. Combining these analyses with results from algal and host genotyping revealed a striking symbiont effect on both the acclimated coral host transcriptome and the magnitude of the thermal stress response. This is the first study that links coral host transcriptomic patterns to the clade content of their algal symbiont community. Our data provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-algal partnerships.
2009-05-31 | GSE15253 | GEO
Project description:Coral reefs are declining globally. Temperature anomalies disrupt coral-algal symbioses at the molecular level, causing bleaching and mortality events. In terrestrial mutualisms, diversity in pairings of host and symbiont individuals (genotypes) results in ecologically and evolutionarily relevant stress response differences. The extent to which such intraspecific diversity provides functional variation in coral-algal systems is unknown. Here we assessed functional diversity among unique pairings of coral and algal individuals (holobionts). We targeted six genetically distinct Acropora palmata coral colonies that all associated with a single, clonal Symbiodinium ‘fitti’ strain in a natural common garden. No other species of algae or other strains of S. ‘fitti’ could be detected in host tissues. When colony branches were experimentally exposed to cold stress, host genotype influenced the photochemical efficiency of the symbiont strain, buffering the stress response to varying degrees. Gene expression differences among host individuals with buffered vs. non-buffered symbiont responses included biochemical pathways that mediate iron availability and oxygen stress signaling—critical components of molecular interactions with photosynthetic symbionts. Spawning patterns among hosts reflected symbiont performance differences under stress. These data are some of the first to indicate that genetic interactions below the species level affect coral holobiont performance. Intraspecific diversity serves as an important but overlooked source of physiological variation in this system, contributing raw material available to natural selection. Note: in the final publication, only ambient and cold treatments are discussed, but there was an additional hot treatment for each genotype at 34C. Most colonies expired after 6 hours, so PAM data could not be collected. The microarray data from 3.5 hours are included here.
2015-10-01 | GSE50926 | GEO
Project description:A mutualistic relationship between reef-building corals and endosymbiotic algae (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. If, and to what extent, differences in algal symbiont clade contents can exert effects on the coral host transcriptome is currently unknown. In this study, we monitored algal physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered coral fragments using a custom cDNA gene expression microarray. Combining these analyses with results from algal and host genotyping revealed a striking symbiont effect on both the acclimated coral host transcriptome and the magnitude of the thermal stress response. This is the first study that links coral host transcriptomic patterns to the clade content of their algal symbiont community. Our data provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-algal partnerships. Sample Collection and Tank Experiment. On July 31 2007, six replicate fragments (9.5 ± 3.5cm2) were collected using hammer and chisel from the upper sun-exposed surface of five different, healthy-looking Montastraea faveolata colonies near Puerto Morelos, Quintana Roo, México (20o52â28.77âN and 86o51â04.53âW). The fragments were transported to the institute within 1 h and divided evenly between two 50 L aquaria (i.e., 3 fragments from each colony were placed into each tank) that received a constant flow of seawater (0.6 L/min). Each aquarium was fit with a water pump connected to a spray-bar to provide constant water movement and aeration. Both aquaria were placed in a common pond with flowing water to buffer diurnal temperature fluctuations, and both aquaria were acclimated to the same shaded ambient light condition. All coral fragments were mounted on plasticene and kept at a depth of 7 cm. From 10 to 19 August 2007, both aquaria received an average water temperature of 27.9 ± 0.6oC (as recorded by HOBO Light/Temperature Data Loggers, Onset Corp.). Beginning on 11 August, dark-adapted maximum quantum yields for charge separation (Fv/Fm) were measured at dusk for all coral fragments using a DIVING-Pulse Amplitude Modulated (PAM) fluorometer (Walz, Germany). Photosynthetically active radiation (PAR) was measured at noon and averaged 318 ± 129 µmol m-2 s-1. From 20 to 21 August 2007, all coral fragments were brought inside during the passage of Hurricane Dean. On 22 August, the experiment was reconstituted, and acclimation continued on 23 August and lasted until 1 September. During this time, both aquaria received a mean water temperature of 28.5 ± 0.8oC, and mean PAR of 371 ± 169 µmol m-2 s-1. On the night of 1 September, control time point samples from five different colonies were collected from each tank (Figure 1), before one 200-Watt aquarium heater was turned on in the treatment aquarium. A second heater was turned on 3 days later. During the thermal stress experiment, the control aquarium received mean water temperature of 28.8 ± 1.2oC; the heated aquarium, 31.5 ± 1.1oC. During the thermal stress experiment, tanks received mean PAR of 420 ± 152 µmol m-2 s-1. On 11 September, and 19 October, one sample each from five different colonies was collected from each tank for the bleaching and recovery time point, respectively. Microarray Gene Expression Analysis of Coral Host Gene Expression. For the biologically replicated time series experiment, a pool of RNA from all control tank fragments was used as a reference RNA sample, against which each sample from the treatment tank was competitively hybridized. All control and heat-stressed samples were competitively hybridized against the reference RNA. Dye swaps were not performed, as any dye bias present is equal in all comparisons to the reference. Note: Samples VALUEs used for statistical analysis of differential expression. GSE15253_shini_cbr_matrix2_norm.txt used for hierarchical clustering.
2010-05-18 | E-GEOD-15253 | 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 (3˚C 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.
2009-10-31 | GSE16151 | GEO
Project description:Given the overwhelming evidence that symbiont genotypes differentially affect host processes such as growth, bleaching susceptibility, and nutrient acquisition, we set out to measure gene expression differences in fragments of Montastraea faveolata harboring two different clades of Symbiodinium. On the reefs near Puerto Morelos, México, colonies of M. faveolata are known to shift algal symbiont clade with depth, often associating with clade A at the top, clade B in the middle, and clade C near the bottom of the colony. By measuring photosynthetic efficiency and gene expression in control and heat-stressed fragments containing either clade B, clade C, or a mix of both, we found that: 1) the algal response to thermal stress is due to both host and algal factors; 2) fragments of M. faveolata express different genes in response to sub-bleaching thermal stress depending on algal genotype; 3) the overall effect of heat stress on coral gene expression is less significant than the effect of housing different zooxanthellae types. Overall, we present convincing evidence that different Symbiodinium clades may be functionally distinct, which in turn, greatly influences host gene expression.
2009-05-31 | GSE12809 | GEO
Project description:We subjected three inshore and four offshore genotypes of the coral Orbicella faveolata to 30, 31, 32, or 33ºC for 31 days and measured photochemical efficiency (Fv/Fm), the types and relative abundance of dinoflagellate endosymbionts, and gene expression of the host and symbiont. All inshore coral genotypes, regardless of symbiont type, were significantly more thermotolerant than offshore genotypes based on declines in Fv/Fm. The most heat-tolerant inshore genotype (In1) was dominated by Durusdinium trenchii; all other genotypes were Breviolum-dominated, suggesting local adaptation or acclimatization contributes to the heat tolerance of inshore genotypes. After 31 days of heat stress, all coral genotypes (except In2) had lost most of their Breviolum and became dominated by D. trenchii. Host genotype In1 presented unique expression patterns of genes involved in heat shock response, immunity, and protein degradation. There were few changes in the symbiont transcriptomes of inshore corals under heat stress, but significant changes in symbiont gene expression from the offshore colonies, including increases in ribosomal and photosynthetic proteins. These data show that the differential thermotolerance between inshore and offshore O. faveolata in the Florida Keys is associated with statistically significant differences in both host and symbiont gene expression that provide insights into the mechanisms underlying holobiont heat tolerance.
2024-02-06 | GSE225085 | GEO
Project description:Given the overwhelming evidence that symbiont genotypes differentially affect host processes such as growth, bleaching susceptibility, and nutrient acquisition, we set out to measure gene expression differences in fragments of Montastraea faveolata harboring two different clades of Symbiodinium. On the reefs near Puerto Morelos, México, colonies of M. faveolata are known to shift algal symbiont clade with depth, often associating with clade A at the top, clade B in the middle, and clade C near the bottom of the colony. By measuring photosynthetic efficiency and gene expression in control and heat-stressed fragments containing either clade B, clade C, or a mix of both, we found that: 1) the algal response to thermal stress is due to both host and algal factors; 2) fragments of M. faveolata express different genes in response to sub-bleaching thermal stress depending on algal genotype; 3) the overall effect of heat stress on coral gene expression is less significant than the effect of housing different zooxanthellae types. Overall, we present convincing evidence that different Symbiodinium clades may be functionally distinct, which in turn, greatly influences host gene expression. Six fragments (9.5 ± 3.5cm2) from the top (2.7m), middle (3.7m), and bottom (5.2m) of one massive colony of Montastraea faveolata were collected with a hammer and chisel at âLa Bocanaâ reef near Puerto Morelos, Quintana Roo, Mexico on 31 July 2007. The fragments were divided evenly between two aquaria (50L) that received a constant flow of seawater (~0.64L/min). Each aquarium was fit with a water pump connected to a spray-bar to provide constant water movement and aeration. Both aquaria were placed in a common pond with flowing water to buffer diurnal temperature fluctuations, and both aquaria were exposed to shaded ambient light. All coral fragments were mounted on plasticene and kept at a depth of ~7cm. From 10 to 19 August 2007 (acclimation #1), both aquaria received an average water temperature of 27.9 ± 0.6oC (as recorded by HOBO Light/Temperature Data Loggers by Onset Corp.). Effective quantum yield (ÎF/Fmâ) measurements were taken at noon, and maximum quantum yield (Fv/Fm) measurements were taken at dusk for all 18 coral fragments using a DIVING-PAM (Walz) beginning on 11 August. Photosynthetically active radiation (PAR) was measured at noon and averaged 318 ± 129 umol/m2/sec. From 20 to 21 August 2007, all coral fragments were brought inside during the passage of Hurricane Dean. On 22 August, the experiment was reconstituted, and a second acclimation period began on 23 August and lasted until 1 September. During this time, both aquaria received water at an average temperature of 28.5 ± 0.8oC, and PAR at an average of 371 ± 169 umol/m2/sec. On the night of 1 September, one 200-Watt aquarium heater was turned on in the treatment aquarium, and a second heater was turned on 3 days later. During the thermal stress experiment, the control aquarium received an average water temperature of 28.8 ± 1.2oC; the heated aquarium, 31.5 ± 1.1oC. PAR present during the thermal stress experiment averaged 420 ± 152 uE. On the night of 7 September, all fragments were frozen in liquid nitrogen. Eighteen total microarray hybridizations were performed. A reference RNA sample was created by pooling RNA from all 18 prepâs. All control and heat-stressed samples were competitively hybridized against the reference RNA to the M. faveolata microarray (1,310 features).
2010-05-18 | E-GEOD-12809 | biostudies-arrayexpress
Project description:INTRODUCTION: Rising seawater temperatures are threatening the persistence of coral reefs; where above critical thresholds, thermal stress results in a breakdown of the coral-dinoflagellate symbiosis and the loss of algal symbionts (coral bleaching). As symbiont-derived organic products typically form a major portion of host energy budgets, this has major implications for the fitness and persistence of symbiotic corals. </br> OBJECTIVES: We aimed to determine change in autotrophic carbon fate within individual compounds and downstream metabolic pathways in a coral symbiosis exposed to varying degrees of thermal stress and bleaching. </br> METHODS: We applied gas chromatography–mass spectrometry coupled to a stable isotope tracer (13C), to track change in autotrophic carbon fate, in symbiont and host individually, following exposure to elevated water temperature. </br> RESULTS: Thermal stress resulted in partner-specific changes in carbon fate, which progressed with heat stress duration. We detected modifications to carbohydrate and fatty acid metabolism, lipogenesis, and homeostatic responses to thermal, oxidative and osmotic stress. Despite pronounced photodamage, remaining in hospite symbionts continued to produce organic products de novo and translocate to the coral host. However as bleaching progressed, we observed minimal 13C enrichment of symbiont long-chain fatty acids, also reflected in 13C enrichment of host fatty acid pools. </br> CONCLUSION: These data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products.
2018-12-04 | MTBLS538 | MetaboLights
Project description:Endozoicomonas are prevalent, abundant bacterial associates of marine animal hosts, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify putative interactions within the coral holobiont, we characterized a novel Endozoicomonas isolate and assessed its transcriptomic and proteomic responses to tissue extracts of its native host, the Red Sea coral Acropora humilis, at control and elevated temperatures. We show that host cues stimulated differential expression of genes assumed to be involved in the modulation of the host immune response by Endozoicomonas, such as flagellar assembly genes, ankyrins, ephrins, and serpins. Proteome analysis revealed the upregulation of vitamin B1 and B6 biosynthetic as well as glycolytic processes by Endozoicomonas in response to host cues. We further demonstrate that the inoculation of A. humilis with its native Endozoicomonas strain resulted in enhanced holobiont health metrics, such as host tissue protein content and algal symbiont photosynthetic efficiency. Behavioral, physiological, and metabolic changes in Endozoicomonas may be key to the onset and function of mutualistic interactions within the coral holobiont, and our results suggest that the priming of Endozoicomonas to a symbiotic lifestyle may involve modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas presumably plays an important role in holobiont nutrient cycling and may therefore be implicated in its health, acclimatization, and ecological adaptation.
2022-08-12 | PXD027178 | Pride
Project description:In this study, we examined the very early transcriptional response of aposymbiotic coral larval host (still not engaged in symbiosis) to hyperthermal stress. This experimental setting provided a scenario and opportunity to study the direct effect of environmental stressors on the host cell per se. Using a cDNA microarray constructed for Acropora millepora and Q-RT-PCR assays, we identified a number of genes that were significantly up- and down-regulated with increase of seawater temperature. Down-regulation of several key component of DNA/RNA metabolism was detected implying inhibition of this cellular metabolic process, however the down-regulation of overall protein synthesis was not simple and random, which suggest that the response to stress is a more complicated adjustment to the metabolic needs of the cell. We identified four significant outcomes during the very early hours of the transcriptional response to hyperthermal stress in coral larvae. First, molecular chaperones responded to hyperthermal stress by increasing their expression as expected, but the response was immediate and extremely rapid during the first 3 hours of heat exposure. Secondly, elevated temperature triggers down-regulation of a fluorescent protein homolog, DsRed-type FP, suggesting that this gene might be used as a potential molecular marker for monitoring hyperthermal stress in nature. Thirdly, the downregulation of a coral mannose-binding lectin under hyperthermal stress might compromise the coral immune defense and bring about susceptibility to pathogenic diseases. And lastly, an absence in the response of oxidative stress genes in aposymbiotic coral larvae during the early hours to hyperthermal stress suggest that the up-regulation of cnidarian host oxidative stress genes reported during thermal stress in algal/host symbiosis might be triggered directly by ROS generated by photosynthetic-dysfunctionally algal endosymbionts that diffuse into host cells, as very little ROS seems to be produced by the host cells from thermal-associated host cellular damage.
2009-08-11 | GSE16351 | GEO