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High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)
(Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany)
(Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany)
(Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany)
Swedish Museum of Natural History, Department of Environmental research and monitoring.
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2018 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 1, p. 1469-1481Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018. Vol. 18, no 1, p. 1469-1481
Keywords [en]
cetaceans, genomics/proteomics, mammals, molecular evolution
National Category
Genetics
Research subject
Man and the environment
Identifiers
URN: urn:nbn:se:nrm:diva-2823DOI: 10.1111/1755-0998.12932OAI: oai:DiVA.org:nrm-2823DiVA, id: diva2:1239908
Funder
Swedish Agency for Marine and Water ManagementAvailable from: 2018-08-20 Created: 2018-08-20 Last updated: 2019-02-21Bibliographically approved

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