Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669106 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12835812.fastq.gz | Fastqsanger.gz | |||
| SRR12835813.fastq.gz | Fastqsanger.gz | |||
| SRR12835814.fastq.gz | Fastqsanger.gz | |||
| SRR12835815.fastq.gz | Fastqsanger.gz | |||
| SRR12835816.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea. 17 samples, coral tissue punches from healthy and also from dark-spot-affected Siderastrea Siderea coral in the Virgin Islands and the Dry Tortugas National Parks was collected for comparison of associated bacterial communities
2014-09-30 | E-GEOD-60622 | biostudies-arrayexpress
Project description:Coral disease is one of the major causes of reef degradation and therefore of concern to management and conservation efforts. Dark Spot Syndrome (DSS) was described in the early 1990’s as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease, since they can also be caused by physical injury in some species. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two geographic locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies with normal pigmentation and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip™ G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, however the amplicon pools were overwhelmed by coral 18S rRNA genes from S. siderea. Unlike a similar study on a white-plague-like disease, S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the healthy scleractinian coral S. siderea.
2014-09-30 | GSE60622 | 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:The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms.
2013-07-07 | GSE43335 | GEO
Project description:Background. Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. Conclusions. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft coral species. G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change. RNA seq experiment using Illumina GAIIx to compare sea fans exposed to an Aplanochytrium species compared to controls
2012-08-17 | E-GEOD-40169 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE27022: Microarray studies of darkness stress and bleaching in the Caribbean coral Acropora palmata GSE27024: Microarray studies of darkness stress and bleaching in the Caribbean coral Montastraea faveolata Refer to individual Series
2011-03-22 | E-GEOD-27025 | biostudies-arrayexpress
Project description:Background. Coral reef communities are undergoing marked declines due to a variety of stressors including climate change, eutrophication, sedimentation, and disease. The sea fan coral, Gorgonia ventalina, is a tractable study system to investigate the hypothesis that stressors compromise immunity and lead to onset of disease. Functional studies in Gorgonia ventalina immunity indicate that several key pathways and cellular responses are involved in response to natural microbial invaders, although to date the functional and regulatory pathways remain largely un-neffectors, the primary line of defense in invertebrates. This study used short-read sequencing (Illumina GAIIx) to identify genes involved in the response of G. ventalina to a naturally occurring Aplanochytrium spp. parasite. Results. De novo assembly of the G. ventalina transcriptome yielded 90,230 contigs of which 40, 142 were annotated. RNA-Seq analysis revealed 210 differentially expressed genes in sea fans exposed to the Aplanochytrium parasite. Differentially expressed genes involved in immunity include pattern recognition molecules, anti-microbial peptides, wound repair, and reactive oxygen species. Gene enrichment analysis indicated eight biological processes were enriched representing 36 genes, largely involved with protein translation and energy production. Conclusions. This is the first report using high-throughput sequencing to characterize the host response of a coral to a natural pathogen. Furthermore, we have generated the first transcriptome for a soft coral species. G. ventalina is a non-model species for which few sequences had been previously described, and we were able to annotate a large number of genes and describe their potential roles in immune function. Expression analysis revealed genes important in invertebrate innate immune pathways, as well as those whose role is previously un-described in cnidarians. This resource will be valuable in characterizing G. ventalina immune response to infection and co-infection of pathogens in the context of environmental change.
2012-08-17 | GSE40169 | GEO