Goniopora djiboutiensis breed:coral
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA485872 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Acropora pulchra isolate:Coral host | breed:Not applicable Genome sequencing
| PRJNA1162071 | ENA
Project description:Acropora muricata breed:Reef-building Coral Transcriptome or Gene expression
| PRJNA511733 | ENA
Project description:Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene invertebrate. Fossils of the Caribbean stony coral Orbicella annularis retain total hydrolyzable amino acids of a similar composition to extracts from modern O. annularis skeletons and ~10% of the modern skeletal proteome was sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. The data are rich in acidic amino acids such as aspartate and glutamate typical of skeletal proteins, and one of the four sequenced fossil proteins, a highly acidic protein, has been previously characterized in modern coral skeletons. A combination of degradation, or amino acid racemization inhibition of trypsin digestion, appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
2020-10-27 | PXD017876 | 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:Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene invertebrate. Fossils of the Caribbean stony coral Orbicella annularis retain total hydrolyzable amino acids of a similar composition to extracts from modern O. annularis skeletons and ~10% of the modern skeletal proteome was sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. The data are rich in acidic amino acids such as aspartate and glutamate typical of skeletal proteins, and one of the four sequenced fossil proteins, a highly acidic protein, has been previously characterized in modern coral skeletons. A combination of degradation, or amino acid racemization inhibition of trypsin digestion, appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic mand biotic responses to paleoenvironments.
2020-10-27 | PXD017816 | 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. 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:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128374 | GEO
Project description:The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data
2019-03-16 | GSE128373 | GEO
Project description:Background: The Malnad Gidda are unique dwarf Bos indicus cattle native to heavy rainfall Malnad and coastal areas of Karnataka in India. These cattle are highly adapted to harsh climatic conditions and are more resistant to Foot and Mouth disease as compared to other breeds of B.indicus. Since the first genome reference became available from B.taurus Hereford breed, only a few other breeds have been genotyped using high-throughput platforms. Also despite the known reports on high diversity within indicine breeds as compared to taurine breeds, only one draft genome of Nellore and horn transcriptome of Kankrej breed were sequenced at base level resolution. Because of the special characteristics Malnad Gidda possess, it becomes the choice of breed among many indicine cows to study at molecular level and genotyping. Results: Sequencing mRNA from the PBMCs isolated from blood of one selected Malnad Gidda bull resulted in generation of 55 million paired-end reads of 100bp length. Raw sequencing data is processed to trim the adaptor and low quality bases, and are aligned against the whole genome and transcript assemblies of Bos taurus UMD 3.1 and Bos indicus (Nellore breed) respectively. About 72% of the sequenced reads from our study could be mapped against the B.taurus genome where as only 41% of reads could be mapped against the Bos indicus transcript assembly. Transcript assembly from the alignment carried out against the annotated B.taurus UMD 3.1 genome resulted in identification of ~10,000 genes with significant expression (FPKM>1). In a similar analysis against the B.indicus Kankrej assembled transcripts we could identify only ~6,000 transcripts. From the variant analysis of the sequencing data we found ~10,000 SNPs in coding regions among which ~9,000 are novel and ~6,400 are amino acid changing. Conclusions: For the first time we have genotyped and explored the transcriptome of B.indicus Malnad Gidda breed. A comparative analysis of mapping the RNA-Seq data against the available reference genome and transcript sequences is demonstrated. An enhanced utility of transcript sequencing could be achieved by improving or completing the sequence assembly of any B.indicus breed to better characterize the indicine breeds for productivity features and selective breeding.
2016-12-31 | GSE71182 | GEO
Project description:Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene invertebrate. Fossils of the Caribbean stony coral Orbicella annularis retain total hydrolyzable amino acids of a similar composition to extracts from modern O. annularis skeletons and ~10% of the modern skeletal proteome was sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. The data are rich in acidic amino acids such as aspartate and glutamate typical of skeletal proteins, and one of the four sequenced fossil proteins, a highly acidic protein, has been previously characterized in modern coral skeletons. A combination of degradation, or amino acid racemization inhibition of trypsin digestion, appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
2020-10-27 | PXD017880 | Pride