Supporting data for “The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization”
Dataset type: Imaging, Genomic, Transcriptomic
Data released on July 11, 2017
Du X; Fan G; Jiao Y; Zhang H; Guo X; Huang R; Zheng Z; Bian C; Deng Y; Wang Q; Wang Z; Liang X; Liang H; Shi C; Zhao X; Sun F; Hao R; 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. https://doi.org/10.5524/100240
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., Zheng, Z., Bian, C., Deng, Y., Wang, Q., Wang, Z., Liang, X., Liang, H., Shi, C., Zhao, X., Sun, F., Hao, R., Bai, J., Liu, J., … Liu, X. (2017). The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization. GigaScience, 6(8). https://doi.org/10.1093/gigascience/gix059 (PubMed:28873964)
Accessions (data included in GigaDB):
BioProject: PRJNA283019
PRIDE: PXD006786
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
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E | Pinctada fucata martensii | Description:RNA extracted from unfertilized eggs (... Alternative accession-SRA Sample:SAMN07276824 Age:0 ... |
206411 | ||
Fe | Pinctada fucata martensii | Geographic location (country and/or sea,region):Ch... Description:RNA extracted from fertilised eggs, 30... Alternative accession-SRA Sample:SAMN07276825 ... |
206411 | ||
B | Pinctada fucata martensii | Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276826 Age:5 hours after fertilization ... |
206411 | ||
G | Pinctada fucata martensii | Geographic location (country and/or sea,region):Ch... Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276827 ... |
206411 | ||
ET | Pinctada fucata martensii | Sex:undetermined Geographic location (country and/or sea,region):Ch... Description:RNA extracted from fertilised eggs, at... ... |
206411 | ||
T | Pinctada fucata martensii | Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276829 Age:16 hours after fertilization ... |
206411 | ||
D | Pinctada fucata martensii | Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276830 Age:19 hours after fertilization ... |
206411 | ||
DF | Pinctada fucata martensii | Geographic location (country and/or sea,region):Ch... Age:4 days after fertilization Description:RNA extracted from fertilised eggs, at... ... |
206411 | ||
EU | Pinctada fucata martensii | Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276832 Life stage:Early umbo larvae ... |
206411 | ||
EL | Pinctada fucata martensii | Description:RNA extracted from fertilised eggs, at... Alternative accession-SRA Sample:SAMN07276833 Age:28 days after fertilization ... |
206411 |
Click on a table column to sort the results.
Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 835 B | 2017-07-11 | MD5 checksum: 028024d88faf70b3fbcc612c9b4b00d7 |
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abundance of quinoproteins (stained purple) in the nacre matrix revealed by a NBT/glycinate assay | Image | UNKNOWN | 227.07 kB | 2017-07-11 | MD5 checksum: 791811dc13ccf8517a8c5297b9a536bc |
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chitin in the shell matrix of C. gigas stained green with Calcofluor White M2R | Image | UNKNOWN | 3.14 MB | 2017-07-11 | MD5 checksum: 109fb8fbe8f5aaa958f5eb2757b4a9f0 |
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chitin in the shell matrix of P. f. martensii stained green with Calcofluor White M2R | Image | UNKNOWN | 2.47 MB | 2017-07-11 | MD5 checksum: 61dc070af1e514298d1d1c8ae0c6e089 |
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shell matrix extracted from the nacre of P. f. martensii | Image | UNKNOWN | 118.95 kB | 2017-07-11 | MD5 checksum: 61c0532a25c7d290e47ce72bc40ae981 |
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shell matrix extracted from the the prismatic of C. gigas | Image | UNKNOWN | 182.18 kB | 2017-07-11 | MD5 checksum: 0d0cc1235d9c0ea2e60a8484638b4f3d |
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secretory cells in the mantle pallium of P. f. martensii | Image | UNKNOWN | 298.94 kB | 2017-07-11 | MD5 checksum: af4bf0e80a7cb451e7ec9de1d502c65b |
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secretory cells in the mantle pallium of C. gigas | Image | UNKNOWN | 133.58 kB | 2017-07-11 | MD5 checksum: 9248aaae50a444dcebe9fe4a566c6712 |
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zipped folder of all microscope image | Mixed archive | UNKNOWN | 6.32 MB | 2017-07-11 | MD5 checksum: f4b3dfce918107afb36b1c7db62cd818 |
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results of CEGMA annotation | Annotation | GFF | 327.08 kB | 2017-07-11 | MD5 checksum: 21cdbfb4be3a4f1c7119d9c6e92de8fc |
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 |
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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 |
November 9, 2022 | Manuscript Link updated : 10.1093/gigascience/gix059 |