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Genomic and transcriptomic landscapes of independent invasions of the Pacific Oyster Crassostrea gigas

ABSTRACT: Genomic and transcriptomic landscapes of independent invasions of the Pacific Oyster Crassostrea gigas

PROVIDER: PRJEB38693 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4193380.fastq.gz	Fastqsanger.gz
	ERR4193390.fastq.gz	Fastqsanger.gz
	ERR4193400.fastq.gz	Fastqsanger.gz
	ERR4193410.fastq.gz	Fastqsanger.gz
	ERR4193420.fastq.gz	Fastqsanger.gz

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Transcriptome sequencing of Pacific oyster Crassostrea gigas

Project description:Deep sequencing of mRNA from Pacific oyster Crassostrea gigas

2014-07-26 | GSE31011 | GEO

Genomic and transcriptomic landscapes of independent invasions of the Pacific Oyster Crassostrea gigas

Project description:Upon colonizing new habitats invasive species face a series of new selection pressures as a result of changing abiotic conditions and novel biotic interactions with native species. These new selection pressures can be accommodated by different mechanism that act on different levels and across different time scales: 1) By changing transcriptomic profiles species can react by plasticity within individual physiological limitations. 2) Invasive populations can adapt by fixing beneficial genetic variants in response to the newly encountered selection pressures. Here, we compare the genomic and transcriptomic landscapes of two independent invasions of the Pacific Oyster Crassostrea gigas into the North Sea. In detail, we combine high density full genome resequencing and low density ddRAD on the genomic level with RNAseq on the transcriptomic level to reveal outlier loci (SNPs) indicative of adaptation, as well as transcriptomic profiles from a translocation experiment to show immediate physiological reactions. The low congruence between differentially regulated genes and outlier loci indicates that different processes act on the different time scales. By contrasting population outlier loci and population specific transcriptomic profiles we can thus identify relevant processes acting during different phases of the invasive process, which will allow to take a glimpse at the traits and processes characterizing successful invasions.

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miRNA of Pacific oyster Crassostrea gigas for different organs and developmental stages

Project description:miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages.

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Transcriptome sequencing of Pacific oyster Crassostrea gigas

Project description:Deep sequencing of mRNA from Pacific oyster Crassostrea gigas Competent larvae of Crassostrea gigas were treated with epinephrine solution, and then sampled at different time intervals. For shell damage experiment, shell were broken and then tissues were sampled at different time intervals.

2014-07-26 | E-GEOD-31011 | biostudies-arrayexpress

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Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas

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Transcriptomic response of the Pacific oyster Crassostrea gigas to hypoxia

Project description:Marine intertidal organisms commonly face hypoxic stress during low tide emersion; moreover, eutrophic conditions and sediment nearness could lead to hypoxic phenomena; it is indeed important to understand the molecular processes involved in the response to hypoxia. In this study the molecular response of the Pacific oyster Crassostrea gigas to prolonged hypoxia (2 mg O2 L-1 for 20 d) was investigated under experimental conditions. A transcriptomic approach was employed using a cDNA microarray of 9058 C. gigas clones to highlight the genetic expression patterns of the Pacific oyster under hypoxic conditions. Lines of oysters resistant (R) and susceptible (S) to summer mortality were used in this study. This is the first study employing microarrays to characterize the genetic markers and metabolic pathways responding to hypoxic stress in C. gigas.

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miRNA of Pacific oyster Crassostrea gigas for different organs and developmental stages

Project description:miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages. Two RNA pools were created and sequenced by mixing the samples before and after the developmental stage "D shaped larvae". Then ten developmental samples and eleven samples from 7 organs were sequenced.

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Proteomic analysis of Pacific oyster (Crassostrea gigas) mucus during Vibrio infection

Project description:This study aimed to identify the protein composition of mucus in Crassostrea gigas (Pacific oyster) and analyze the proteomic changes during Vibrio ZJ-51 infection. Mucus samples were collected from control (C1–C3) and infected oysters (T1–T3). Using LC-MS/MS, over 4000 proteins were identified from oyster mucus. Differential expression analysis revealed significant proteomic alterations in response to Vibrio infection, providing insights into the host-pathogen interaction and potential defense mechanisms. This study contributes to the understanding of oyster mucus composition and its response to bacterial challenge.

2025-07-29 | PXD064651 | Pride

Transcriptome response to salinity stress in the Pacific oyster Crassostrea gigas

Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates.

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Exosomal shuttle protein in Pacific oyster Crassostrea gigas during bacterial stimulation

Project description:As marine invertebrates, oysters lack adaptive immunity and employ innate immunity as the front line and lmost the solo defense mechanism to protect them against invaders. Accumulating research achievements demonstrated that exosomes could act as innate immune effectors that contribute to host defense mechanism. To better understand the immune functions of exosomes in Crassostrea gigas against bacterial stimulation, iTRAQ was applied to explore the global protein changes of exosomes in oyster after Staphylococcus aureus and Vibrio splendidus stimulation.

2019-11-06 | PXD011539 | Pride

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