Ontology highlight
ABSTRACT:
PROVIDER: PRJNA999033 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25433400_1.fastq.gz | Fastqsanger.gz | |||
| SRR25433400_2.fastq.gz | Fastqsanger.gz | |||
| SRR25433401_1.fastq.gz | Fastqsanger.gz | |||
| SRR25433401_2.fastq.gz | Fastqsanger.gz | |||
| SRR25433402_1.fastq.gz | Fastqsanger.gz |
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Project description:The Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community.
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Project description:The Pacific oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, can tolerate temperature fluctuations. Heat shock transcription factor 1 (HSF1) plays an important role in the process of resistance of thermal stress. However, HSF1 has not been fully characterized in the Pacific oyster. C. gigas with an expansion of heat shock protein (HSP) 70. In this study, we analyzed genes regulated by HSF1 in response to heat shock by Chromatin immunoprecipitation followed sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to specific binding sites of HSF1, and peaks were annotated to nearest genes. In Gene Ontology analysis, HSF1 target genes was related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific oyster.
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Project description:Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably in Northern Europe. To explore adaptation on reproductive traits of population considered as invasive, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark. A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several genes differentially expressed between the Danish and French progenies, and with an intermediate expression level in hybrids (additive behavior). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism known to be implicated in coordinated control of reproduction. Our results suggest adaptation of invasive populations during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, fertility and gamete quality. A common garden experiment was performed in order to compare progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Progenies were reared under standard hatchery and nursery conditions until gonadal maturation. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011).
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Project description:Hox and ParaHox genes encode transcription factors with conserved similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. We thus conducted experiments to show that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is also a direct target of Pdx in the Pacific oyster. We report that oyster has a diversity of insulin-related genes including one co-expressed with Pdx in the endodermal layer of oyster digestive tissue. Transcriptome analysis reveals functional similarity of this tissue to vertebrate pancreas. Using ATAC-seq we identify a Pdx homeodomain binding site upstream of the endodermally-expressed oyster insulin-related gene and using cell culture demonstrate that oyster Pdx acts as a transcriptional activator through this site. These data argue that a classic homeodomain-target gene interaction dates back to the base of Bilateria.
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