Coral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1001615 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25503020_1.fastq.gz | Fastqsanger.gz | |||
| SRR25503020_2.fastq.gz | Fastqsanger.gz | |||
| SRR25503021_1.fastq.gz | Fastqsanger.gz | |||
| SRR25503021_2.fastq.gz | Fastqsanger.gz | |||
| SRR25503022_1.fastq.gz | Fastqsanger.gz |
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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: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.
2014-03-26 | GSE27624 | GEO
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.
2009-04-01 | GSE14923 | GEO
Project description:Background: The molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host Results: In the current study, we utilised dual RNA-seq approach to study both symbiont and coral transcriptomes during symbiosis establishment. The transcriptomic response of C. goreaui to the symbiotic state was complex, the most obvious feature of which was extensive and generalized downregulation of gene expression. Included in this “symbiosis-derived transcriptional repression” were a range of stress response and immune-related genes. In contrast, a range of genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of C. goreaui suggests that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship is established at the larval stage. The coral data imply the involvement of some SCRiP family members in the colonisation process and support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses. Conclusions: This study provides novel insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.
2020-08-13 | GSE145030 | GEO
Project description:Endozoicomonas coral host response
| PRJNA753662 | ENA
Project description:Similar to many marine invertebrates, scleractinian corals experience a dramatic morphological transformation, as well as a habitat switch, upon settlement and metamorphosis. At this time, planula larvae transform from non-calcifying, demersal, motile organisms into sessile, calcifying, benthic juvenile polyps. We performed a gene expression microarray analysis between planulae, aposymbiotic primary polyps, and symbiotic adult tissue to elucidate the molecular mechanisms underlying coral metamorphosis and early stages of calcification in the Robust/Short clade scleractinian coral Montastraea faveolata. Among the annotated genes, the most abundant upregulated transcripts in the planula stage are involved in protein synthesis, chromatin assembly and mitochondrial metabolism; the polyp stage, morphogenesis, protein catabolism and organic matrix synthesis; and the adult stage, sexual reproduction, stress response and symbiosis. Additionally, our results indicate that metamorphosis in M. faveolata planulae is likely regulated by: 1) a mechanism that resembles that described for hydrozoan cnidarians involving the neuropeptide LWamide; and 2) conserved cell adhesion and apoptosis mechanisms. Our results also suggest that calicoblast differentiation pathways may be regulated by transforming growth factors from the BMP family and Notch signalling pathway. We also present evidence showing that the planula and adult transcriptomes are more similar to each other than to the polyp trancriptome. Lastly, our results point to a large number of uncharacterized adult coral-specific genes likely involved in coral-specific functions such as symbiosis and calcification.
2009-05-06 | GSE15962 | 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:We tested the thermal tolerance of coral larvae with heat-evolved and wild-type strains and explored the molecular mechanisms for the differential thermal tolerance with gene expression patterns. This archive provides the raw data of the RNA sequencing.
2020-05-21 | GSE133082 | GEO
Project description:Background: The molecular machinery underpinning the establishment of this relationship is not well understood. This is especially true of the symbiont side, as previous attempts to understand the interaction between coral larvae and Symbiodiniaceae have focused nearly exclusively on the host Results: The transcriptomic response of C. goreaui to the symbiotic state was complex, the most obvious feature of which was extensive and generalized downregulation of gene expression. Included in this “symbiosis-derived transcriptional repression” were a range of stress response and immune-related genes. In contrast, a range of genes implicated in metabolism were upregulated in the symbiotic state. Consistent with previous ecological studies, this transcriptomic response of C. goreaui suggests that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship is established at the larval stage Conclusions: This study provides novel insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle, with important implications for understanding the establishment of symbiosis between corals and their dinoflagellate partners.
2020-05-31 | GSE143202 | GEO
Project description:The endosymbiotic interaction established by cnidarians and photosynthetic dinoflagellate algae is the foundation of coral reef ecosystems. This essential interaction is globally threatened to breakdown by anthropogenic disturbance. As such, it is compelling to understand the molecular mechanisms underpinning the cnidarian-algal association. We investigated phosphorylation-mediated protein signaling as a mechanism of regulation of the cnidarian-algal interaction, and we report on the generation of the first phosphoproteome for the coral model system Aiptasia. Using mass spectrometry-based phosphoproteomics in data-independent acquisition (DIA) allowed consistent quantification of over 3,000 phosphopeptides totaling more than 1,600 phosphoproteins across aposymbiotic (symbiont-free) and symbiotic anemones. Additionally, to allow for discrimination between translational regulation and post-translational phosphorylation, we generated a total proteome dataset from the same anemones and used it for phosphopeptide normalization against protein amount. While quantification of protein phosphorylation relied upon the generation of a spectrum library generated by data-dependent acquisition (DDA), total protein quantification in DIA was conducted "library-free" (directDIA) in SpectronautX. DirectDIA allowed consistent quantification of 20,215 peptides, totaling 4,121 proteins (3,518 protein groups) across biological samples.
2019-11-06 | PXD014076 | Pride