Dataset Information

Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (Crassostrea gigas) Microbiota from the Puget Sound Region in the United States.

ABSTRACT: This is the first study analyzing Pacific oyster microbiota in the Puget Sound estuarine system using a next-generation sequencing method. Taxonomic analysis indicated that Tenericutes, Chlamydiae, Proteobacteria, and Firmicutes were the most abundant phyla. Small numbers of operational taxonomic units (OTUs) belonging to the Vibrio genus were detected in all the oyster microbiome samples.

SUBMITTER: Li Z

PROVIDER: S-EPMC5465617 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (Crassostrea gigas) Microbiota from the Puget Sound Region in the United States.

Li Zhen Z Wang Leyi L

Genome announcements 20170608 23

This is the first study analyzing Pacific oyster microbiota in the Puget Sound estuarine system using a next-generation sequencing method. Taxonomic analysis indicated that Tenericutes, Chlamydiae, Proteobacteria, and Firmicutes were the most abundant phyla. Small numbers of operational taxonomic units (OTUs) belonging to the Vibrio genus were detected in all the oyster microbiome samples. ...[more]

PMID: 28596398

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Project description:BackgroundLow salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas is considered to be tolerant to relative low salinity. The genes that regulate C. gigas responses to osmotic stress were monitored using the next-generation sequencing of whole transcriptome with samples taken from gills. By RNAseq technology, transcript catalogs of up- and down-regulated genes were generated from the oysters exposed to low and optimal salinity seawater.Methodology/principal findingsThrough Illumina sequencing, we reported 1665 up-regulated transcripts and 1815 down-regulated transcripts. A total of 45771 protein-coding contigs were identified from two groups based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes that changed expression significantly were highly represented in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlighted genes related to osmoregulation, signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytoskeleton and cell cycle.Conclusions/significanceThrough more than 1.5 million sequence reads and the expression data of the two libraries, the study provided some useful insights into signal transduction pathways in oysters and offered a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will not only provide a better understanding of the molecular mechanisms about the response to osmotic stress of the oysters, but also facilitate research into biological processes to find underlying physiological adaptations to hypoosmotic shock for marine invertebrates.

Dataset Information

Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (Crassostrea gigas) Microbiota from the Puget Sound Region in the United States.

Publications

Metagenomic 16S rRNA Sequencing Analysis of Pacific Oyster (<i>Crassostrea gigas</i>) Microbiota from the Puget Sound Region in the United States.

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