Coral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA274945 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR069604.fastq.gz | Fastqsanger.gz | |||
| SRR069605.fastq.gz | Fastqsanger.gz | |||
| SRR069606.fastq.gz | Fastqsanger.gz | |||
| SRR069607.fastq.gz | Fastqsanger.gz | |||
| SRR069608.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: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:The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. To test the hypothesis that larval transcription profiles reflect population specific responses to thermal stress, symbiont-free gametes of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico and raised under normal and elevated temperatures. These populations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among thousands of genes were simultaneously characterized using microarrays, allowing investigation of gene expression patterns among wild populations under stressful environmental conditions. Results show site-specific signatures of gene expression in larvae of a reef-building coral from different parts of its range (despite low genetic divergence), and reveal both local and general components of stress response during later stages of larval development. These results provide evidence of site-specific variation in the face of gene flow, which may represent functional genetic variation in different subpopulations, and support the idea that coral host genomes may indeed house the adaptive potential needed to deal with changing environmental conditions.
2010-06-23 | GSE19998 | GEO
Project description:This experiment assessed the natural gene expression variation present between colonies of the Indo-Pacific reef-building coral Acropora millepora, and additionally explored whether gene expression differed between two different intron haplotypes according to intron 4-500 in a carbonic anhydrase homolog. This study found no correspondence between host genotype and transcriptional state, but found significant intercolony variation, detecting 488 representing unique genes or 17% of the total genes analyzed. Such transcriptomic variation could be the basis upon which natural selection can act. Underlying variation could potentially allow reef corals to respond to different environments. Whether this source of variation and the genetic responses of corals and its symbionts will allow coral reefs to cope to the rapid pace of global change remains unknown. A. millepora colonies were brought to a common garden in the reef lagoon, i.e. under the same environmental conditions. This common garden combined with acclimatization removes environmental effects on the physiology of the coral colonies. For the comparison of the two intron haplotypes, we applied a multiple dye-swap microarray design for the two groups of coral colonies (N=3 per group) defined based on the two genotypes resolved with the use of intron 4-500 (Fig. 1). To also examine the intra-haplotype variation we added a loop design nested to the above multiple dye-swap design, where three samples per colony were included. Colonies 1, 2, and 3 are of intron 4-500 haplotype 1; colonies 4, 5, and 6 are haplotype 2.
2013-04-08 | E-GEOD-42684 | biostudies-arrayexpress
Project description:Despite their early evolutionary divergence, reef-building corals exhibit complex circadian responses to diurnal, lunar and annual changes in the conditions around them. Understanding circadian regulation in reef-building corals is, however, complicated by the presence of photosynthetic endosymbionts that have a profound physiochemical influence on the intracellular environment. How corals tune their animal-based clock machinery to respond to external cues while at the same time responding to internal physiological changes imposed by the symbiont is not clear. We explore this issue using microarray analysis to dissect genes governed directly by the circadian machinery from those responding indirectly as a consequence of changing internal oxygen tensions. Three coral colonies were sampled at 4 hr intervals during two consecutive days under an ambient light/dark (LD) cycle and under constant darkness (DD). In total 72 arrays were hybridized, as each array represented a sample from a treatment and a time point (n=3).
2011-04-20 | E-GEOD-21658 | biostudies-arrayexpress
Project description:This experiment assessed the natural gene expression variation present between colonies of the Indo-Pacific reef-building coral Acropora millepora, and additionally explored whether gene expression differed between two different intron haplotypes according to intron 4-500 in a carbonic anhydrase homolog. This study found no correspondence between host genotype and transcriptional state, but found significant intercolony variation, detecting 488 representing unique genes or 17% of the total genes analyzed. Such transcriptomic variation could be the basis upon which natural selection can act. Underlying variation could potentially allow reef corals to respond to different environments. Whether this source of variation and the genetic responses of corals and its symbionts will allow coral reefs to cope to the rapid pace of global change remains unknown.
2013-04-08 | GSE42684 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE12809: Symbiodinium clade content drives host transcriptome more than thermal stress in the coral Montastraea faveolata (part 1) GSE15253: Symbiodinium clade content drives host transcriptome more than thermal stress in the coral Montastraea faveolata (part 2) Refer to individual Series
2010-05-18 | E-GEOD-15262 | biostudies-arrayexpress
Project description:Since the discovery of Chromera velia as a novel coral-associated microalga, this organism has attracted interest because of its unique evolutionary position between the photosynthetic dinoflagellates and the parasitic apicomplexans. The nature of the relationship between Chromera and its coral host is controversial. Is it a mutualism, from which both participants benefit, or is Chromera a parasite, harming its host? To better understand the interaction, larvae of the common Indo-Pacific reef-building coral Acropora digitifera were experimentally infected with Chromera and the impact on the host transcriptome assessed at 4, 12, and 48 h post-infection using Illumina RNA-Seq technology. The transcriptomic response of the coral to Chromera was complex and implies that host immunity is strongly suppressed, and both phagosome maturation and the apoptotic machinery modified. These responses differ markedly from those described for infection with a competent strain of the coral symbiont Symbiodinium, instead resembling those of vertebrate hosts to parasites and/or pathogens such as Mycobacterium tuberculosis. Consistent with ecological studies suggesting that the association may be accidental, the transcriptional response of A. digitifera larvae leads us to conclude that Chromera is more likely to be a coral parasite, commensal, or accidental bystander, but certainly not a beneficial mutualist
2017-08-16 | GSE102664 | GEO
Project description:The potential to adapt to a changing climate depends in part upon the standing genetic variation present in wild populations. In corals, the dispersive larval phase is particularly vulnerable to the effects of environmental stress. Larval survival and response to stress during dispersal and settlement will play a key role in the persistence of coral populations. To test the hypothesis that larval transcription profiles reflect population specific responses to thermal stress, symbiont-free gametes of the scleractinian coral Montastraea faveolata were collected from Florida and Mexico and raised under normal and elevated temperatures. These populations have been shown to exchange larvae frequently enough to prevent significant differentiation of neutral loci. Differences among thousands of genes were simultaneously characterized using microarrays, allowing investigation of gene expression patterns among wild populations under stressful environmental conditions. Results show site-specific signatures of gene expression in larvae of a reef-building coral from different parts of its range (despite low genetic divergence), and reveal both local and general components of stress response during later stages of larval development. These results provide evidence of site-specific variation in the face of gene flow, which may represent functional genetic variation in different subpopulations, and support the idea that coral host genomes may indeed house the adaptive potential needed to deal with changing environmental conditions. 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 collected in Mexico. For samples from Mexico we used three technical replicates for each treatment temperature, for samples from Florida three biological replicates were used for each treatment temperature, except for the high temperature samples at day two where only two replicates were available due to high larval mortality at that temperature. Common reference samples were labeled with Cy3, temperature treatment 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.
2010-06-23 | E-GEOD-19998 | biostudies-arrayexpress
Project description:<p>Benthic organisms sustain coral reefs through their growth and metabolism, but less is known about how their released metabolites influence reef seawater microorganisms. To investigate metabolite composition of benthic exudates and their ecological significance for reef microbial communities, we harvested exudates from six species of Caribbean benthic organisms including stony corals, octocorals, and an invasive encrusting algae, and subjected these exudates to untargeted and targeted metabolomics approaches using liquid chromatography-mass spectrometry. Incubations with reef seawater microorganisms were conducted to monitor changes in microbial community composition using 16S rRNA gene sequencing and abundance in relation to exudate source and three specific metabolites. Exudates tended to be enriched in amino acids, nucleosides, and vitamins, indicating that benthic organisms contribute labile organic matter to reefs. The phytohormone indole-3-acetic acid was detected in octocoral exudates, suggesting that this metabolite facilitates microbial interactions within and outside of benthic organisms. Exudate compositions were species-specific and significantly enriched in the indole class of metabolites. Microbial abundances and specific microbial taxa responded differently in relation to exudates from stony corals and octocorals, demonstrating the link between benthic organismal composition, metabolite exudates, and microbial growth. Conversely, microbial communities did not respond to additions of the individual metabolites, suggesting that reef microorganisms likely provide diverse metabolite pools that support microbial growth. This work provides novel information about the metabolites released from common Caribbean benthic organisms and indicates that the recent shifts in benthic composition from stony to octocorals alter exudate composition and likely impact microbial community composition and function on coral reefs.</p><p><br></p><p><strong>UPLC-MS Metabolite collection incubation assays</strong> are reported in the current study <strong>MTBLS2855</strong></p><p><strong>UPLC-MS Metabolite uptake incubation assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/editor/study/MTBLS3286' rel='noopener noreferrer' target='_blank'><strong>MTBLS3286</strong></a></p>
2022-08-22 | MTBLS2855 | MetaboLights