Genomic data from the Pacific oyster (Crassostrea gigas).

Dataset type: Genomic, Transcriptomic
Data released on July 12, 2012

Fang X; Li L; Luo R; Xu F; Wang X; Zhu Y; Yang L; Huang Z (2012): Genomic data from the Pacific oyster (Crassostrea gigas). GigaScience. http://dx.doi.org/10.5524/100030

DOI10.5524/100030

The Pacific oyster (Crassostrea gigas) belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. In this study, DNA was extracted from an oyster derived from four generations of full-sib mating. Short-reads and a fosmid-pooling strategy were used for sequencing and assembly of the oyster genome. DNA extracted from the inbred oyster and another wild oyster was used for resequencing analysis. Finally, RNA-seq and small RNA from different organs at different developmental stages were extracted for developmental studies.

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., … Qi, H. (2012). The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490(7418), 49–54. doi:10.1038/nature11413 (PubMed: 22992520)
Yu, H., Zhao, X., & Li, Q. (2016). Genome-wide identification and characterization of long intergenic noncoding RNAs and their potential association with larval development in the Pacific oyster. Scientific Reports, 6(1). doi:10.1038/srep20796

Accessions (data included in GigaDB):

GENBANK: AFTI01000000
SRA: SRA040229
SRA: SRA043580
GEO: GSE31012





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
oyster29159Pacific oysterPacific oysterCrassostrea gigas
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
oysterTranscriptome sequenceFASTQ1.37 GB2012-07-12
oysterTranscriptome sequenceFASTQ1.36 GB2012-07-12
oysterTranscriptome sequenceFASTQ876.11 MB2012-07-12
oysterOtherEXCEL101 KB2012-07-12
oysterTranscriptome sequenceFASTQ586.34 MB2012-07-12
oysterTranscriptome sequenceFASTQ697.36 MB2012-07-12
oysterTranscriptome sequenceFASTQ637.22 MB2012-07-12
oysterTranscriptome sequenceFASTQ694.83 MB2012-07-12
oysterTranscriptome sequenceFASTQ660.09 MB2012-07-12
oysterTranscriptome sequenceFASTQ692.34 MB2012-07-12
Displaying 1-10 of 201 File(s).
Date Action
October 19, 2015 File oyster.v9.glean.final.rename.gff.pep.gz updated
October 19, 2015 File oyster.v9.fa.gz updated
October 19, 2015 File oyster.v9.glean.final.rename.gff.cds.gz updated
October 19, 2015 File oyster.v9.glean.final.rename.gff.gz updated
October 20, 2015 File ED1.fq.gz updated
October 20, 2015 File ED2.fq.gz updated
October 22, 2015 File BGI_Illumina_RNA-seq_oyster_mRNA.xls updated
November 4, 2015 File Dgl_1.fq.gz updated
November 4, 2015 File Dgl_2.fq.gz updated
November 5, 2015 File Gil_1.fq.gz updated
November 5, 2015 File Gil_2.fq.gz updated
February 18, 2016 Manuscript Link added : 10.1038/srep20796