Supporting data for “The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization”

Dataset type: Genomic, Transcriptomic, Imaging
Data released on July 11, 2017

Bian C; Deng Y; Du X; Fan G; Guo X; Hao R; Huang R; Jiao Y; Liang H; Liang X; Shi C; Sun F; Wang Q; Wang Z; Zhang H; Zhao X; Zheng Z; Bai J; Liu J; Chen W; Liang J; Liu W; Xu Z; Shi Q; Xu X; Zhang G; Liu X (2017): Supporting data for “The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization” GigaScience. http://dx.doi.org/10.5524/100240

DOI10.5524/100240

Nacre, the iridescent material found in pearls and shells of molluscs, is formed through an extraordinary process of matrix-assisted biomineralization. Despite recent advances, many parts of the biomineralization process and its evolutionary origin remain a mystery. The pearl oyster Pinctada fucata martensii is a well-known master of biomineralization, but the molecular mechanisms underlie its production of remarkable shells and pearls is not fully understood. We sequenced the highly polymorphic genome of the pearl oyster and conducted multi-omic and biochemical studies to probe nacre formation. We identified a large set of novel proteins participating in matrix-framework formation, many in expanded families, including components similar to that found in vertebrate bones such as collagen-related VWA-containing proteins (VWAP), fibronectin, chondroitin sulfotransferases and regulatory elements. Considering that there are only collagen-based matrices in vertebrate bones and chitin-based matrices in most invertebrate skeletons, the presence of both chitin and elements of collagen-based matrices in nacre matrices suggests that elements of chitin- and collagen-based matrices are deeply rooted and might be part of an ancient biomineralizing matrix. Our results expand the current shell matrix-framework model and provide new insights into the evolution of diverse biomineralization systems.

Additional details

Read the peer-reviewed publication(s):

Du, X., Fan, G., Jiao, Y., Zhang, H., Guo, X., Huang, R., … Liu, X. (2017). The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization. GigaScience, 6(8), 1–12. doi:10.1093/gigascience/gix059

Accessions (data included in GigaDB):

BioProject: PRJNA283019
PRIDE: PXD006786





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
EU206411  Pinctada fucata martensii Description:RNA extracted from fertilised eggs, at...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276832
...
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F206411  Pinctada fucata martensii Description:RNA extracted from adult foot tissue
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276843
...
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Fe206411  Pinctada fucata martensii Description:RNA extracted from fertilised eggs, 30...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276825
...
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G206411  Pinctada fucata martensii Description:RNA extracted from fertilised eggs, at...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276827
...
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GENOMIC DNA sample206411  Pinctada fucata martensii Description:DNA extracted from adult adductor mus...
Analyte type:DNA
Alternative accession-SRA Sample:SAMN03603317
...
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Gi206411  Pinctada fucata martensii Description:RNA extracted from adult gill tissue
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276842
...
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Go206411  Pinctada fucata martensii Description:RNA extracted from adult gonad tissu...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276841
...
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He206411  Pinctada fucata martensii Description:RNA extracted from adult hepatopancre...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276839
...
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J206411  Pinctada fucata martensii Description:RNA extracted from fertilised eggs, at...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276835
...
+
ME206411  Pinctada fucata martensii Description:RNA extracted from adult mantle edge ...
Analyte type:RNA
Alternative accession-SRA Sample:SAMN07276838
...
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Displaying 11-20 of 24 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherRAW872.03 MB2017-07-11
OtherRAW632.64 MB2017-07-11
OtherRAW648.96 MB2017-07-11
OtherRAW587.3 MB2017-07-11
OtherRAW664.34 MB2017-07-11
OtherRAW650.75 MB2017-07-11
OtherRAW620.14 MB2017-07-11
OtherRAW606.68 MB2017-07-11
OtherRAW621.49 MB2017-07-11
OtherRAW545.18 MB2017-07-11
Displaying 1-10 of 123 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China X Du 31272635
National Natural Science Foundation of China Y Deng 31372526
National Natural Science Foundation of China Y Jiao 31672626
Modern Agro-industry Technology Research System X Du CARS-48
Date Action
July 11, 2017 Dataset publish
August 3, 2017 File LC_MSMS_result_v2.zip updated
August 3, 2017 File Pinctada.gene.final.chr.gff.gz updated
August 3, 2017 File Pinctada.gene_cufflink.final.chr.cds.gz updated
August 3, 2017 File Pinctada.gene.final.chr.pep.gz updated
August 3, 2017 File Pinctada.chromosome.fasta.gz updated
August 3, 2017 File Pinctada.gene.final.chr.cds.gz updated
August 3, 2017 File Pinctada.gene_cufflink.final.chr.pep.gz updated
August 3, 2017 File microscope_image.rar updated
August 3, 2017 File Pinctada.CEGMA.gff updated
August 3, 2017 File readme.txt updated
August 3, 2017 File Pinctada.RAD.genotype.gz updated
August 3, 2017 File Pinctada_RAD_sample.csv updated
August 3, 2017 File Pinctada_phylogeny.cds.4d.phy updated
August 3, 2017 File Pinctada_phylogeny.cds.phase1.phy updated
August 3, 2017 File Pinctada_proteome_dataset.csv updated
August 3, 2017 File Pinctada_transcriptome_dataset.csv updated
November 13, 2017 Manuscript Link added : 10.1093/gigascience/gix059