Supporting data for "The Gene-Rich Genome of the Scallop Pecten maximus"
Dataset type: Genomic
Data released on March 19, 2020
Kenny NJ; Dudchenko O; James K; Betteridge E; Corton C; Dolucan J; Mead D; Oliver K; Omer A; Pelan S; Ryan Y; Sims Y; Skelton J; Smith M; Torrance J; Weisz D; Wipat A; Aiden EL; Howe K; Williams ST (2020): Supporting data for "The Gene-Rich Genome of the Scallop Pecten maximus" GigaScience Database. https://doi.org/10.5524/100726
The King Scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and its ubiquity means that it plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies and fisheries management.
Here we report the genome sequencing of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10x Chromium and Hi-C data, and its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb, and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.
The genome assembly of Pecten maximus and its annotated gene set provide a high-quality platform for a wide range of investigations, including studies on such disparate topics as shell biomineralization, pigmentation, vision and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
Additional details
Read the peer-reviewed publication(s):
- Kenny, N. J., McCarthy, S. A., Dudchenko, O., James, K., Betteridge, E., Corton, C., Dolucan, J., Mead, D., Oliver, K., Omer, A. D., Pelan, S., Ryan, Y., Sims, Y., Skelton, J., Smith, M., Torrance, J., Weisz, D., Wipat, A., Aiden, E. L., … Williams, S. T. (2020). The gene-rich genome of the scallop Pecten maximus. GigaScience, 9(5). https://doi.org/10.1093/gigascience/giaa037 (PubMed:32352532)
Additional information:
www.dnazoo.org/assemblies/Pecten_maximus
http://dx.doi.org/10.6084/m9.figshare.10311068
Accessions (data included in GigaDB):
BioSample: SAMEA994736
BioSample: SAMN12747920
Assembly: GCA_902652985.1
Accessions (data not in GigaDB):
BioProject: PRJNA242355
BioProject: PRJNA298284
BioProject: PRJEB17629
Click on a table column to sort the results.
Table SettingsSample ID | Common Name | Scientific Name | Sample Attributes | Taxonomic ID | Genbank Name |
---|---|---|---|---|---|
SAMEA994736 | Pecten maximus | Local environmental context:wild caught [FOODON_00... Geographic location (latitude and longitude):nor r... Sex:hermaphrodite [PATO:0001340] ... |
6579 | ||
GSM4417291Pm_mantle_a | Pecten maximus | Alternative accession-GEO:GSE147107 Analyte type:RNA Tissue:mantle [UBERON:0006575] ... |
6579 | ||
GSM4417292Pm_mantle_b | Pecten maximus | Alternative accession-BioSample:SAMN14390691 Alternative accession-BioProject:N/A Alternative accession-GEO:GSE147107 ... |
6579 |
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 | 4.43 kB | 2020-03-19 | MD5 checksum: 77ca74ec013788a2b4b3c972bb96c562 |
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Read quality assessment, FastQC | Other | HTML | 1.21 MB | 2020-03-19 | MD5 checksum: 0ef3cd6ed153a66adb0e9667b0062806 |
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Hard masked ('N') repeats version of genome | Genome sequence | FASTA | 183.07 MB | 2020-03-19 | MD5 checksum: 8da1d89d0e722f7b45e0a635577ca605 |
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Soft masked (lower case) repeats version of genome | Genome sequence | FASTA | 257.62 MB | 2020-03-19 | MD5 checksum: 30aca34d0e00d6dda233506548df12fe |
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Best blast hit of all gene models - no filtering of gene models | Other | TEXT | 10.93 MB | 2020-03-19 | MD5 checksum: 418ca0dabd67dd13456a72215ca81786 |
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CDS sequence of all gene models - no filtering of gene models | Coding sequence | FASTA | 34.79 MB | 2020-03-19 | MD5 checksum: 4db64cca7303978f63f70b068665c54b |
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Amino acid sequence of all gene models - no filtering of gene models | Protein sequence | FASTA | 22.34 MB | 2020-03-19 | MD5 checksum: 1dea816233487da5264d6ef3dba9b954 |
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GFF3 annotation file of all gene models - no filtering of gene models | Annotation | UNKNOWN | 22.78 MB | 2020-03-19 | MD5 checksum: 2fca95f4e7412cf24a425c8bd27a3419 |
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GTF annotation file of all gene models - no filtering of gene models | Annotation | UNKNOWN | 22.63 MB | 2020-03-19 | MD5 checksum: 257f2d92d7ea73a470bbe3791dd96201 |
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CDS sequence of filtered gene models - Final gene set | Coding sequence | FASTA | 17.05 MB | 2020-03-19 | MD5 checksum: 26cd1409b7f9480f562464723b78c900 |
Funding body | Awardee | Award ID | Comments |
---|---|---|---|
Natural History Museum(NHM) | ST Williams | SDR17012 | |
H2020 Marie Skłodowska-Curie Actions | NJ Kenny | 750937 | |
Wellcome Trust | S McCarthy | WT207492 | |
National Science Foundation | E Aiden | PHY1427654 | Physics Frontiers Center Award |
Welch Foundation | E Aiden | Q-1866 | |
National Institutes of Health | E Aiden | U01HL130010 | 4D Nucleome Grant |
DNA Genotek (CA) | E Aiden | UM1HG009375 | |
U.S. Department of Agriculture | E Aiden | 2017-05741 | Agriculture and Food Research Initiative Grant |
Marie Curie Alumni Association | NJ Kenny | N/A |
Date | Action |
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March 19, 2020 | Dataset publish |
April 8, 2020 | Manuscript Link added : 10.1093/gigascience/giaa037 |
October 7, 2022 | Manuscript Link updated : 10.1093/gigascience/giaa037 |
February 9, 2023 | Link updated : Assembly:GCA_902652985.1 |