Supporting data for "Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis".
Dataset type: Genomic
Data released on April 25, 2016
Long KA; Nossa CW; Sewell MA; Putnam NH; Ryan JF (2016): Supporting data for "Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis". GigaScience Database. https://doi.org/10.5524/100194
There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water vascular system, mutable collagenous tissues, and endoskeletons of high magnesium calcite. To our knowledge, the only echinoderm species with a genome sequence available to date is Strongylocentrotus pupuratus (Echinoidea). The availability of additional echinoderm genome sequences is crucial for understanding the biology of these animals.
Here we present assembled draft genomes of the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis from Illumina sequence data with coverages of 12.5x, 22.5x, and 21.4x, respectively.
These data provide a resource for mining gene superfamilies, identifying non-coding RNAs, confirming gene losses, and designing experimental constructs. They will be important comparative resources for future genomic studies in echinoderms.
Additional details
Read the peer-reviewed publication(s):
- Long, K. A., Nossa, C. W., Sewell, M. A., Putnam, N. H., & Ryan, J. F. (2016). Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis. GigaScience, 5(1). https://doi.org/10.1186/s13742-016-0125-6
Additional information:
http://ryanlab.whitney.ufl.edu/genomes/
Accessions (data included in GigaDB):
BioProject: PRJEB10600
BioProject: PRJEB10682
BioProject: PRJEB10339
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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SAMEA3518466 | Patiriella regularis | Geographic location (latitude):-38.84734 Collection date:13 Jan 2013 Geographic location (longitude):174.8382 ... |
46519 | ||
SAMEA3518467 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518468 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518469 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518470 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518471 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518472 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518473 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518474 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 | ||
SAMEA3518475 | Patiriella regularis | Geographic location (latitude):-38.84734 Geographic location (longitude):174.8382 Geographic location (country and/or sea,region):Ko... ... |
46519 |
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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Readme | TEXT | 4.27 kB | 2016-04-01 | MD5 checksum: fbf885490e84eeee9957105b1fcce9b8 |
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Australostichopus mollis protein sequences of gene models (version 0.01) | Protein sequence | FASTA | 3.59 MB | 2016-04-01 | MD5 checksum: 10c999426440c43048103382b9325a1d |
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Australostichopus mollis augustus annotations (version 0.01) | Annotation | GFF | 43.47 MB | 2016-04-01 | MD5 checksum: 1939bcc3a731d3e63b71f72ecf25dbc0 |
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Australostichopus mollis genome assembly (version 0.01) | Genome sequence | FASTA | 1.33 GB | 2016-04-01 | MD5 checksum: 9f1069ceff69edacbe64884c64d8480c |
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Ophionereis fasciata protein sequences of gene models (version 0.01) | Protein sequence | FASTA | 7.86 MB | 2016-04-01 | MD5 checksum: d27fa39cc3e4edbe4e53e349f69fce27 |
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Ophionereis fasciata augustus annotations (version 0.01) | Annotation | GFF | 57.81 MB | 2016-04-01 | MD5 checksum: 0bdabc2b63d4603fc8c3fe2d03827711 |
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Ophionereis fasciata genome assembly (version 0.01) | Genome sequence | FASTA | 1.27 GB | 2016-04-01 | MD5 checksum: 4bafa5e23f5939652fc55e6eeb088b45 |
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Patiriella regularis genome assembly (version 0.01) | Genome sequence | FASTA | 1.01 GB | 2016-04-01 | MD5 checksum: 879f443fa5111324da18b62ff9444076 |
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Patiriella regularis protein sequences of gene models (version 0.01) | Protein sequence | FASTA | 104.73 kB | 2016-04-01 | MD5 checksum: 13af4d0eb679d80eb5d91122d13497ac |
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Ophionereis fasciata augustus annotations (version 0.01) | Annotation | GFF | 451.89 kB | 2016-04-01 | MD5 checksum: 37d172f661de64f9db4d06157d0d40ba |
Funding body | Awardee | Award ID | Comments |
---|---|---|---|
National Science Foundation | DBI-1156528 | Kyle Long |
Date | Action |
---|---|
April 25, 2016 | Dataset publish |
May 12, 2016 | Manuscript Link added : 10.1186/s13742-016-0125-6 |
May 12, 2016 | File readme.txt updated |
November 11, 2022 | File Ofas.01.gff.gz updated |
November 11, 2022 | File Preg.01.gff.gz updated |
November 11, 2022 | File Amol.01.gff.gz updated |
November 11, 2022 | File Ofas.02.gff.gz updated |
November 14, 2022 | Update file type to fasta, data type to protein sequence; File Amol.01.aa.gz updated |
November 14, 2022 | Update file type to fasta, data type to protein sequence; File Preg.01.aa.gz updated |
November 14, 2022 | Update data type to genome assembly; File Patiriella_regularis_genome.0.01.fa updated |
November 14, 2022 | Update file type to fasta, data type to protein sequence; File Ofas.01.aa.gz updated |
November 14, 2022 | Update data type to genome assembly; File Australostichopus_mollis.0.01.fa updated |
November 14, 2022 | Update file format to fasta, data type to protein sequence; File Ofas.02.aa.gz updated |
November 14, 2022 | Update data type to genome assembly; File Ophionereis_fasciata_genome.0.02.fa updated |
November 14, 2022 | Update data type to genome assembly;File Ophionereis_fasciata_genome.0.01.fa updated |