Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1124244 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29525310_1.fastq.gz | Fastqsanger.gz | |||
| SRR29525310_2.fastq.gz | Fastqsanger.gz | |||
| SRR29525311_1.fastq.gz | Fastqsanger.gz | |||
| SRR29525311_2.fastq.gz | Fastqsanger.gz | |||
| SRR29525312_1.fastq.gz | Fastqsanger.gz |
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Project description:The Crown-of-Thorns starfish (COTS), Acanthaster planci, is a highly fecund predator of reef-building corals distributed throughout the Indo-Pacific. COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of the reef ecosystems thus increasing their susceptibility to climate change. We sequenced genomes of A. planci from the Great Barrier Reef, Australia (GBR) and Okinawa, Japan (OKI) to guide identification of species-specific peptide communication with potential applications in mitigation strategies. The genome-encoded proteins excreted and secreted into the surrounding seawater by COTS forming aggregations and by those escaping the predatory giant triton snail, Charonia tritonis, were identified LC-MS/MS.
2017-04-06 | PXD005409 | Pride
Project description:Increasing seawater’s calcium concentration has shown to increase reef building (scleractinian) coral’s calcification rates. In this way the expression of the genes that are associated with the calcification process also altered and, thus can be identified. Needless to say that the overall gene repertoire that participate in the coral calcification process and its molecular mechanisms have not yet been revealed, although sporadic genes that are related to the process have been discovered and investigated. In this study, nubbins of the Red Sea scleractinian coral, Stylophora pistillata were treated with increased calcium concentrations seawater (addition of 100 gm/L) and the genes that have been up-regulated were compared to the genes expression profile of corals with natural seawater calcium concentration. Measurements of AT were taken at mid-day (11:00) and in nighttime (23:00), to record the calcification rates of coral individuals under normal and increased calcium seawater concentrations. In order to reveal the gene involved in the calcification process, S. pistillata fragments of normal and of increased calcium concentrations were sampled for microarray RNA transcriptional profiling at two time-points (mid-day and nighttime).Results of this study have revealed that Smad genes may play a role in the coral skeletal growth apparatus. This study show that the calcification molecular mechanism is conserved Among identified genes are large group of genes that are characterized in the TGF-b/BMP signal transduction pathways which have been revealed in other organisms to participate in bone and cartilage tissue development molecular processes.
2017-06-29 | GSE87159 | GEO
Project description:Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we test the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fish species will respond to these increased temperatures and which genes are important for resistance and adaptation to elevated temperatures is not known. Microarray technology may help identify candidate genes for thermal stress resistance in coral reef fishes. Results from a comparative genomic DNA hybridisation experiment and direct sequence comparisons indicate that for most genes there is significant sequence similarity between P. moluccensis and D. rerio, suggesting that the D. rerio array is applicable to P. moluccensis. Heterologous microarray experiments on heat-stressed P. moluccensis identified changes in transcript abundance at 120 gene loci, with many genes involved in protein processing, transcription, and cell growth. Changes in transcript abundance for a selection of candidate genes were confirmed by quantitative real-time PCR. We have demonstrated that heterologous microarrays can be successfully employed to study non-model organisms. Such a strategy thus greatly enhances the applicability of microarray technology to the field of environmental and functional genomics and will be useful for investigating the molecular basis of thermal adaptation in coral reef fishes. Keywords: stress response, comparative genomic hybridization (CGH)
2006-04-30 | GSE4047 | 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.
2009-08-31 | GSE15088 | 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:Hawai'i coral reef seawater, environmental DNA metabarcoding
| PRJNA607318 | ENA
Project description:Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we test the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fish species will respond to these increased temperatures and which genes are important for resistance and adaptation to elevated temperatures is not known. Microarray technology may help identify candidate genes for thermal stress resistance in coral reef fishes. Results from a comparative genomic DNA hybridisation experiment and direct sequence comparisons indicate that for most genes there is significant sequence similarity between P. moluccensis and D. rerio, suggesting that the D. rerio array is applicable to P. moluccensis. Heterologous microarray experiments on heat-stressed P. moluccensis identified changes in transcript abundance at 120 gene loci, with many genes involved in protein processing, transcription, and cell growth. Changes in transcript abundance for a selection of candidate genes were confirmed by quantitative real-time PCR. We have demonstrated that heterologous microarrays can be successfully employed to study non-model organisms. Such a strategy thus greatly enhances the applicability of microarray technology to the field of environmental and functional genomics and will be useful for investigating the molecular basis of thermal adaptation in coral reef fishes. Keywords: stress response, comparative genomic hybridization (CGH) Common reference design [Stress response_P. moluccensis]: four individual treatment fish (heat-stressed) are contrasted in four microarray hybridisations against a pooled control consisting of four fish kept at ambient temperature. All eight fish employed in this analysis were wild-captured and are biological replicates. The experiment included dye-swap, i.e. stressed fish were labelled red in two hybridisations and green in the other two hybridisations. Common reference design [CGH_P. moluccensis and D. rerio]: four individual P. moluccensis gDNA samples are contrasted in four microarray hybridisations against a pooled gDNA sample consisting of three D. rerio. The experiment included dye-swaps.
2010-06-11 | E-GEOD-4047 | biostudies-arrayexpress
Project description:Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.
2016-02-01 | MTBLS281 | MetaboLights
Project description:Corals especially the reef-building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. Corals especially the reef-building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. In the present study, five protocols were compared for protein extraction from stony corals.
2022-07-24 | PXD006334 | Pride