High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena)
Abstract 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 popu...
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crwiley:10.1111/1755-0998.12932 2024-06-02T08:07:46+00:00 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 Universität Potsdam 2018 http://dx.doi.org/10.1111/1755-0998.12932 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12932 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12932 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 18, issue 6, page 1469-1481 ISSN 1755-098X 1755-0998 journal-article 2018 crwiley https://doi.org/10.1111/1755-0998.12932 2024-05-03T11:22:30Z Abstract 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 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. Article in Journal/Newspaper Harbour porpoise Phocoena phocoena Wiley Online Library Kattegat ENVELOPE(9.692,9.692,63.563,63.563) Molecular Ecology Resources 18 6 1469 1481 |
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Wiley Online Library |
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English |
description |
Abstract 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 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. |
author2 |
Universität Potsdam |
format |
Article in Journal/Newspaper |
author |
Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph |
spellingShingle |
Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
author_facet |
Autenrieth, Marijke Hartmann, Stefanie Lah, Ljerka Roos, Anna Dennis, Alice B. Tiedemann, Ralph |
author_sort |
Autenrieth, Marijke |
title |
High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
title_short |
High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
title_full |
High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
title_fullStr |
High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
title_full_unstemmed |
High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise ( Phocoena phocoena) |
title_sort |
high‐quality whole‐genome sequence of an abundant holarctic odontocete, the harbour porpoise ( phocoena phocoena) |
publisher |
Wiley |
publishDate |
2018 |
url |
http://dx.doi.org/10.1111/1755-0998.12932 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12932 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12932 |
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_source |
Molecular Ecology Resources volume 18, issue 6, page 1469-1481 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.12932 |
container_title |
Molecular Ecology Resources |
container_volume |
18 |
container_issue |
6 |
container_start_page |
1469 |
op_container_end_page |
1481 |
_version_ |
1800752899145334784 |