Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1280067 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR34074914_1.fastq.gz | Fastqsanger.gz | |||
| SRR34074914_2.fastq.gz | Fastqsanger.gz | |||
| SRR34074915_1.fastq.gz | Fastqsanger.gz | |||
| SRR34074915_2.fastq.gz | Fastqsanger.gz | |||
| SRR34074916_1.fastq.gz | Fastqsanger.gz |
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Project description:Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
2012-11-22 | GSE37279 | GEO
Project description:Marine sponges are essential for coral reefs to thrive and harbour a diverse microbiome that is thought to contribute to host health. Although the overall function of sponge symbionts has been increasingly described, in-depth characterisation of each taxa remains challenging, with many sponge species hosting up to 3,000 distinct microbial species. Recently, the sponge Ianthella basta has emerged as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other minor taxa. Here, we retrieved metagenome assembled genomes (MAGs) for >90% of I. basta’s microbial community which allowed us to make a complete metabolic reconstruction of the sponge’s microbiome, identifying metabolic complementarity between microbes, as well as the importance of symbionts present in low abundance. We also mined the metagenomes for putative viral sequences, highlighting the contribution of viruses to the overall metabolism of the sponge, and complement this data with metaproteomic sequencing to identify active metabolic pathways in both prokaryotes and viruses. This data now allows us to use I. basta as a model organism for studying host-microbe interactions and provides a basis for future (genomic) manipulative experiments.
2023-02-24 | PXD032278 | Pride
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. Coral monitoring data and disease prevention/treatment efforts from recent years have identified individual Orbicella faveolata that possess high, moderate, or low resistance to stony coral tissue loss disease (SCTLD). Ninety samples of high, moderate, or low SCTLD resistance were collected from 3 reefs for bottom-up LC-MS/MS analysis (n=30 for each resistance category).
2022-01-13 | PXD030923 | Pride
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
2024-11-24 | GSE263620 | GEO
Project description:<p>Sponges are sessile filter-feeders that can process vast amounts of water and are known to influence the chemistry of the surrounding seawater. There has been limited work however to understand the extent to which sponges alter dissolved organic matter (DOM), yet in areas where sponges are abundant, sponges may contribute significantly to the reef seawater profile of DOM. This work provides an in-depth examination of six prevalent sponges on Caribbean reefs and how they alter DOM and other seawater nutrients. Incurrent and excurrent seawater samples were collected for each of the six sponge species and processed for: inorganic nutrients, fluorescent dissolved organic matter (fDOM), untargeted and targeted metabolomics, and particulate matter by flow cytometry. Sponges were sampled from two coral reef sites in the Florida Keys (Florida, USA): Looe Key reef and Wonderland reef in the southern Florida Keys. We found higher that sponges altered a relatively small subset of the DOM profile and were a net sink of most mass features from untargeted metabolomics. However, sponges also released some putatively labile metabolites and processed DOM in a species-specific manner. These results provide additional support for the large impact that sponges have in the dissolved nutrient profile on coral reefs and provide support for a species-specific impact, with some species altering the DOM profile, fDOM profile, and/or inorganic nutrients to a greater extent than other species. These results have implications for better understanding the influence of the sponge community on coral reef nutrient dynamics.</p>
2025-10-21 | MTBLS13194 | MetaboLights