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Shrimp gut metagenome

ABSTRACT: Analysis of the shrimp hepatopancreas and water microbiota in the rearing of L. vannamei

PROVIDER: PRJNA602773 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10962600_1.fastq.gz	Fastqsanger.gz
	SRR10962600_2.fastq.gz	Fastqsanger.gz
	SRR10962700_1.fastq.gz	Fastqsanger.gz
	SRR10962700_2.fastq.gz	Fastqsanger.gz
	SRR10962800_1.fastq.gz	Fastqsanger.gz

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Shrimp transcriptome analysis after exposure to recombinant Vibrio parahaemolyticus PirA and PirB toxins

Project description:Vibrio parahaemolyticus is a Gram-negative bacterium commonly found in marine and estuarine environments. Acute hepatopancreatic necrosis disease (AHPND) caused by this bacterium is an ongoing problem among shrimp farming industries. V. parahaemolyticus proteins PirA and PirB have been determined to be major virulence factors that induce AHPND. In this study, Pacific white shrimp (Litopenaeus vannamei) were challenged with recombinant PirA and PirB by a reverse gavage method and then at 30 m, 1, 2, 4, and 6 h time points, the hepatopancreas of five individual shrimp were removed and placed into RNA later. We conducted RNA sequencing of the hepatopancreas samples from a no PirA/B control (n = 5) and PirA/B-treated shrimp at the different time intervals (n=5). We evaluated the different gene expression patterns between the time groups to the control with a focus on identifying differences in innate immune function.

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Project description:Here we used microarrays to characterize changes in global gene expression in the hepatopancreas of Pacific white shrimp, Litopenaeus vannamei, exposed to short term (4 h) hypoxia (H) or hypercapnic hypoxia (HH) or long term (24 h) H or HH, compared to animals in air-saturated water (normoxia). The transcriptomes of crustaceans exposed to low O2 and high CO2 contained both shared and treatment-specific signature genes (q M-bM-^IM-$ 0.01, FC M-bM-^IM-% 1.5), with shifts characteristic of metabolic depression rather than anaerobic metabolism. Down-regulated signature genes dominated the transcript profile in three of the four treatments (H 4 h, H 24 h, 4 h HH); many of these genes were involved in amino acid or RNA metabolism or in translation, including several tRNA synthetases. Unique patterns of gene expression such as increased lipid metabolism and hemocyanin synthesis (H 24 h) and initiation of apoptosis (24 h HH) were tied to specific treatments. This work contributes insight to the effects that human perturbations might have on estuarine organisms, and the importance of examining the impacts of environmentally relevant combinations of hypoxia and hypercapnia on estuarine populations. L. vannamei were exposed for 4 or 24 hours to one of the following conditions: normoxia, hypoxia or hypercapnic hypoxia. Hepatopancreas tissue from individual animals was dissected, total RNA extracted, labelled and hybridized to oligonucleotide microarrays with probes for 21,864 L. vannamei unigenes. Treatments were repeated until a total of 7 biological replicates was obtained for each time:treatment combination, except for the 24 h normoxia group, represented by 6 replicates.

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