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Metadata: Genome sequence and gene annotations of the Patagonion toothfish 2019
Abstract:
Outputs include the genome of the Patagonian toothfish, including the sequence of the genome and gene annotations and raw sequencing data, which includes the genome and transcriptome sequenced from multiple different tissues, using different sequencing technologies. Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited.
Data holder:
Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)
| Other details | ||
| Internal code | Internally assigned metadata identifier | 9659 |
| Title | The title is used to provide a brief and precise description of the dataset such as 'Date', 'Originating organisation/programme', 'Location' and 'Type of survey'. All acronyms and abbreviations should be reproduced in full. | Genome sequence and gene annotations of the Patagonion toothfish 2019 |
| File Identifier | The File Identifier is a code, preferably a GUID, that is globally unique and remains with the same metadata record even if the record is edited or transferred between portals or tools. | CEFAS4e644fd0-1265-43c1-a759-96a092bd5424 |
| Resource Identifier | This is the code assigned by the data owner. | CEFAS21804 |
| Resource type | The resource type will likely be a dataset but could also be a series (collection of datasets with a common specification) or a service. | dataset |
| Start date | This describes the date the resource starts. This may only be the year if month and day are not known | 2019-08-01 |
| End date | This describes the date the resource ends. This may only be the year if month and day are not known | 2024-05-10 |
| Frequency of updates | This describes the frequency with which the resource is modified or updated i.e. a monitoring programme that samples once per year has a frequency that is described as 'annually'. | notPlanned |
| Abstract | The abstract provides a clear and brief statement of the content of the resource. | Outputs include the genome of the Patagonian toothfish, including the sequence of the genome and gene annotations and raw sequencing data, which includes the genome and transcriptome sequenced from multiple different tissues, using different sequencing technologies. Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. |
| Lineage | Lineage includes the background information, history of the sources of data, data quality statements and methods. | A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (*Dissostichus mawsoni*). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. |
| Related keywords | ||
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Aquaculture |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Genetics | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Agricultural and aquaculture facilities | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Marine Environmental Data and Information Network | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | data.gov.uk | |
| Geographical coverage | ||
| North | The northern-most limit of the data resource in decimal degrees | 52.4595 |
| East | The eastern-most limit of the data resource in decimal degrees | 1.74086 |
| South | The southern-most limit of the data resource in decimal degrees | 52.4581 |
| West | The western-most limit of the data resource in decimal degrees | 1.73881 |
| Responsible organisations | ||
| Role | The point of contact is person or organisation with responsibility for the creation and maintenance of the metadata for the resource. | pointOfContact |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The originator is the person or organisation who created, collected or produced the resource. | originator |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The custodian is the person or organisation that accepts responsibility for the resource and ensures appropriate care and maintenance. If a dataset has been lodged with a Data Archive Centre for maintenance then this organisation is be entered here. | custodian |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The distributor is the person or organisation that distributes the resource. | distributor |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Resource locators | ||
| Locator URL | Web address (URL) that links to the resource | https://data.cefas.co.uk/view/21804 |
| Locator name | Name of the web resource | Cefas Data Portal |
| Dataset constraints | ||
| 20.1 Limitations on Public Access - Access constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 20.2 Limitations on Public Access - Other constraints | noLimitations | |
| 21.1 Conditions for Access and Use - Use constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 21.2 Conditions for Access and Use - Other constraints | http://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_RestrictionCode | |
| Version info | ||
| Date of publication | The publication date of the resource or if previously unpublished the date that the resource was made publicly available via the MEDIN network. | 2024-05-01 |
| Date of last revision | The most recent date that the resource was revised. | 2024-05-10 |
| Date of creation | The date that the resource was created. | 2024-02-07 |
| Harvest date | The date which this record has been (re)harvested from the provider. | 2026-04-12 |
| Metadata date | The date when the content of this metadata record was last updated. | 2024-05-10 |
| Metadata standard name | The name of the metadata standard used to create this metadata | MEDIN |
| Metadata standard version | The version of the MEDIN Discovery Metadata Standard used to create the metadata record | 3.1.1 |