Ontology highlight
ABSTRACT:
PROVIDER: PRJNA802894 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17876402_1.fastq.gz | Fastqsanger.gz | |||
| SRR17876402_2.fastq.gz | Fastqsanger.gz | |||
| SRR17876403_1.fastq.gz | Fastqsanger.gz | |||
| SRR17876403_2.fastq.gz | Fastqsanger.gz | |||
| SRR17876404_1.fastq.gz | Fastqsanger.gz |
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Project description:Branching coral species like the Caribbean Acroporids are long lived and reproduce asexually via breakage of branches. Fragmentation is the dominant mode of local population maintenance for these corals across much of their range. Thus, large genets with many member ramets (colonies) are common. Each of the ramets experiences different microenvironments, especially with respect to light and water flow. Here, we investigate whether colonies that are members of the same genet have different epigenomes because of differences in their microenvironments. The Florida Keys experienced a large- scale coral bleaching event in 2014-2015 caused by high water temperatures. During the event, ramets of the same coral genet bleached differently. Previous work had shown that this was unlikely to be due to their eukaryotic algal symbionts (Symbiodinium ‘fitti’) because each genet of this coral species typically harbors a single strain of S. ‘fitti’. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the host’s genetic background, the position of the sampled polyps within the colonies (e.g. tip versus base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes and thus to a differential bleaching response.
2019-12-05 | GSE124246 | GEO
Project description:Branching coral species like the Caribbean Acroporids are long lived and reproduce asexually via breakage of branches. Fragmentation is the dominant mode of local population maintenance for these corals across much of their range. Thus, large genets with many member ramets (colonies) are common. Each of the ramets experiences different microenvironments, especially with respect to light and water flow. Here, we investigate whether colonies that are members of the same genet have different epigenomes because of differences in their microenvironments. The Florida Keys experienced a large- scale coral bleaching event in 2014-2015 caused by high water temperatures. During the event, ramets of the same coral genet bleached differently. Previous work had shown that this was unlikely to be due to their eukaryotic algal symbionts (Symbiodinium ‘fitti’) because each genet of this coral species typically harbors a single strain of S. ‘fitti’. Characterization of the microbiome via 16S tag sequencing did not provide evidence for a central role of microbiome variation in determining bleaching response. Instead, epigenetic changes were significantly correlated with the host’s genetic background, the position of the sampled polyps within the colonies (e.g. tip versus base of colony), and differences in the colonies’ condition during the bleaching event. We conclude that microenvironmental differences in growing conditions led to long-term changes in the way the ramets methylated their genomes and thus to a differential bleaching response.
2020-12-18 | GSE124256 | GEO
Project description:Short title: Coral Meta-Transcriptomics Reveal Pollutant Stress Background: Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater). Results: RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5). Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral / zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (ie. cytochrome P450 and UDP glucuronosyltransferase 2) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal. Conclusions: Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts.
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Project description:Prokaryotic communities associated with different habitats within coral animals
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Project description:Florida’s coral reefs are currently experiencing a multi-year disease-related mortality event, that has resulted in massive die-offs in multiple coral species. Approximately 21 species of coral, including both Endangered Species Act-listed and the primary reef-building species, have displayed tissue loss lesions which often result in whole colony mortality [Stony Coral Tissue Loss Disease (SCTLD)]. Determining the causative agent(s) of coral disease relies on a multidisciplinary approach since the causation may be a combination of abiotic, microbial or viral agents. Metaproteomics was used to survey changes in the molecular landscape in the coral holobiont with the goal of providing useful information not only in diagnosis, but for prediction and prognosis. Specifically, in the case of SCTLD, defining molecular changes in the coral holobiont will help define disease progression and aid in identifying the causative agent by clearly defining traits of disease progression shared across affected species. Using samples from nine coral species (46 samples total; those appearing healthy, n = 23, and diseased, n = 23), analysis of the coral and its associated microbiome were performed using bottom-up proteomics. Ongoing analysis (including improving coral holobiont genome-based search space) will demonstrate the utility of this approach and help define improved future experiments.
2021-05-21 | PXD026192 | Pride
Project description:Telomere DNA length is a complex trait controlled both by multiple loci and environmental factors. Even though the use of telomere DNA length measurement, as a method of assessing stress accumulation and predicting how this will influence survival, is currently being studied in numerous human cohort studies, the importance of telomere length for stress response in ecological studies remains at its infancy. Here, we investigated the telomere changes occurring in the symbiotic coral Stylophora pistillata that has experienced a continuous darkness over 6 months. This stress condition led to the loss of its symbionts, as what is also observed when bleaching occurs in the field at a large-scale due to climate changes and anthropogenic activities, threatening the worldwide reef ecosystem. We found that the continuous darkness condition was associated to telomere DNA length shortening and a downregulation of the expression of the telomere-associated protein POT2. These results pave the way for future studies on the role of telomere in coral stress response and the importance of telomere dysregulation in endangered coral species
2021-09-20 | GSE171268 | GEO
Project description:Background: Anthozoan cnidarians are amongst the simplest animals at the tissue level of organization, but are surprisingly complex and vertebrate-like in terms of gene repertoire. As major components of tropical reef ecosystems, the stony corals are anthozoans of particular ecological significance. To better understand the molecular bases of both cnidarian development in general and coral-specific processes such as skeletogenesis and symbiont acquisition, microarray analysis was carried out through the period of early development – when skeletogenesis is initiated, and symbionts are first acquired. Methodology/ Principal Findings: Of approximately 5600 unique genes represented on the microarrays, 1084 were differentially expressed (P <0.05) in comparisons between four different stages of coral development, spanning key developmental transitions. Genes of likely relevance to the processes of settlement, metamorphosis, calcification and interaction with symbionts were characterised further and their spatial expression patterns investigated using whole-mount in situ hybridisation. Conclusions/Significance: This study is the first large-scale investigation of developmental gene expression for any cnidarian, and has provided candidate genes for key roles in many aspects of coral biology, including calcification, metamorphosis and symbiont uptake. One surprising finding is that some of these genes have clear counterparts in higher animals but are not present in the closely-related sea anemone Nematostella. A second conclusion is that coral-specific processes (i.e. traits which distinguish corals from their close relatives) may be analogous to similar processes in distantly related organisms. This first large-scale application of microarray analysis demonstrates the potential of this approach for investigating many aspects of coral biology, including the effects of stress and disease. Keywords: developmental
2008-12-05 | GSE11251 | GEO
Project description:This experiment is contains cow organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from three different animals as biological replicates. This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
2012-12-21 | E-MTAB-2798 | biostudies-arrayexpress
Project description:This experiment is contains rat organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from animals of three different strains (Sprague-Dawley, BN/SsNHsd and F344/Cr1). This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
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