Sponge metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA207094 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:In the seabed, chemical defences mediate inter- and intraspecific interactions and may determine organisms’ success, shaping the diversity and function of benthic communities. Sponges represent a prominent example of chemically-defended marine organisms with great ecological success. The ecological factors controlling the production of their defensive compounds and the evolutionary forces that select for these defences remain little understood. Each sponge species produces a specific and diverse chemical arsenal with fish-deterrent, antifouling and antimicrobial properties. However, some small animals (mesograzers), mainly sea slugs, have specialized in living and feeding on sponges. Feeding on chemically-defended organisms provides a strategy to avoid predators, albeit the poor nutritional value of sponges. In order to investigate the mechanisms that control sponge chemical defence, with particular focus on the response to specialist grazers, we investigated the interaction between the sponge Aplysina aerophoba and the sea slug Tylodina perversa. Here we performed controlled experiments and collected sponge samples at different time points (3h, 1d and 6d after treatment). To further elucidate if the sponge response is specific to grazing by T. perversa, we also included a treatment in which sponges were mechanically damaged with a scalpel. We compared gene expression between treatments based on RNA-Seq data.
2022-01-30 | E-MTAB-8601 | biostudies-arrayexpress
Project description:Neopetrotaurines A-C, isoquinoline quinone-linked isoquinoline alkaloids that possess a unique taurine bridge connecting the two bicyclic components, were isolated from a Neopetrosia sp. marine sponge. These new compounds have proton-deficient scaffolds, so their structure elucidation was facilitated by utilizing LR-HSQMBC and HMBC NMR experiments optimized to detect 4- and 5-bond long-range 1H-13C heteronuclear correlations. Neopetrotaurines A-C showed potent inhibition of transcription driven by the oncogenic fusion protein PAX3-FOXO1 in alveolar rhabdomyosarcoma.
2024-03-21 | GSE249431 | GEO
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.
2012-06-01 | GSE27141 | GEO
Project description:In order to compare sponge and eumetazoan (higher animal) body plans, we identified and studied expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). In this species, embryonic development is semi-synchronous within a population, synchronous within individuals, and oocytes and embryos occupy a significant fraction of the volume of the sponges during the reproductive period. RNASeq libraries representing non-reproductive (somatic) tissue slices along the body axis, as well as oocytes, embryos and free swimming larvae were generated from material obtained by sampling throughout the life cycle.
2014-05-01 | E-MTAB-2431 | biostudies-arrayexpress
Project description:miRNA sponge, a special class of miRNA target, has been emerging as a pivotal player in miRNA mediated regulatory network. Currently, the identified miRNA sponge genes mostly act on sequestering conserved miRNAs (e.g. miR-7, miR-145), however, the existence, potential function and evolutionary process of miRNA sponge genes for species-specific miRNA, especially for human specific miRNA, are largely unknown. In this study, we conducted a systematic analysis including sponge gene identification and subsequent function and evolutionary analyses for an authentic human-specific miRNA, miR-941.
2019-01-01 | GSE93716 | GEO
Project description:Marine sponge metagenomes Metagenome
| PRJNA602572 | ENA
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition. Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.
2012-05-31 | E-GEOD-27141 | biostudies-arrayexpress
Project description:In order to compare sponge and eumetazoan (higher animal) body plans, we identified and studied expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). In this species, embryonic development is semi-synchronous within a population, synchronous within individuals, and oocytes and embryos occupy a significant fraction of the volume of the sponges during the reproductive period. RNASeq libraries representing non-reproductive (somatic) tissue slices along the body axis, as well as oocytes, embryos and free swimming larvae were generated from material obtained by sampling throughout the life cycle.
2014-05-01 | E-MTAB-2430 | biostudies-arrayexpress