Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive subtle differentiation among populations, b...
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ftdans:oai:easy.dans.knaw.nl:easy-dataset:109182 2023-07-02T03:32:29+02:00 Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph 2018-07-11T17:24:00.000+02:00 http://nbn-resolving.org/urn:nbn:nl:ui:13-8s-rohn https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:109182 unknown doi:10.5061/dryad.vr021gq/1 http://nbn-resolving.org/urn:nbn:nl:ui:13-8s-rohn doi:10.5061/dryad.vr021gq https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:109182 OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf Life sciences medicine and health care 2018 ftdans https://doi.org/10.5061/dryad.vr021gq/110.5061/dryad.vr021gq 2023-06-13T13:31:21Z The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using just 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization, and motif prediction. Within the predicted genes we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny, and conservation. Other/Unknown Material Harbour porpoise Phocoena phocoena Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) Kattegat ENVELOPE(9.692,9.692,63.563,63.563) |
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Open Polar |
collection |
Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) |
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unknown |
topic |
Life sciences medicine and health care |
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Life sciences medicine and health care Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
topic_facet |
Life sciences medicine and health care |
description |
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using just 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization, and motif prediction. Within the predicted genes we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny, and conservation. |
author |
Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph |
author_facet |
Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph |
author_sort |
Autenrieth, Marijke |
title |
Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
title_short |
Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
title_full |
Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
title_fullStr |
Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
title_full_unstemmed |
Data from: High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) |
title_sort |
data from: high quality whole genome sequence of an abundant holarctic odontocete, the harbour porpoise (phocoena phocoena) |
publishDate |
2018 |
url |
http://nbn-resolving.org/urn:nbn:nl:ui:13-8s-rohn https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:109182 |
long_lat |
ENVELOPE(9.692,9.692,63.563,63.563) |
geographic |
Kattegat |
geographic_facet |
Kattegat |
genre |
Harbour porpoise Phocoena phocoena |
genre_facet |
Harbour porpoise Phocoena phocoena |
op_relation |
doi:10.5061/dryad.vr021gq/1 http://nbn-resolving.org/urn:nbn:nl:ui:13-8s-rohn doi:10.5061/dryad.vr021gq https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:109182 |
op_rights |
OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf |
op_doi |
https://doi.org/10.5061/dryad.vr021gq/110.5061/dryad.vr021gq |
_version_ |
1770272078248804352 |