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  • 1. Autenrieth, Marijke
    et al.
    Hartmann, Stefanie
    Lah, Ljerka
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Dennis, Alice B.
    Tiedemann, Ralph
    High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 1, p. 1469-1481Article in journal (Refereed)
    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.

  • 2.
    Marquina, Daniel
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Andersson, Anders
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998Article in journal (Refereed)
  • 3.
    Marquina, Daniel
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Esparza-Salas, Rodrigo
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Roslin, Tomas
    Swedish University of Agricultural Sciences.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches2019In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, p. 1516-1530Article in journal (Refereed)
  • 4.
    Schmidt, Stefan
    et al.
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Taeger, Andreas
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Morinière, Jérôme
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Liston, Andrew
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Blank, Stephan
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Kramp, Katja
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Kraus, Manfred
    Nürnberg, Germany.
    Schmidt, Olga
    SNSB-Zoologische Staatssammlung München, Munich, Germany.
    Heibo, Erik
    Lierskogen, Norway.
    Prous, Marko
    Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany.
    Nyman, Tommi
    Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
    Malm, Tobias
    Swedish Museum of Natural History, Department of Zoology.
    Stahlhut, Julie
    Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada.
    Identification of sawflies and horntails (Hymenoptera, ‘Symphyta’) through DNA barcodes: successes and caveats2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, p. 670-685Article in journal (Refereed)
    Abstract [en]

    The ‘Symphyta’ is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of ‘Symphyta’, mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non-European origin. The utility of barcoding for species identification and taxonomy of ‘Symphyta’ is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.

  • 5. van der Valk, Tom
    et al.
    Durazo, Frida Lona
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Guschanski, Katerina
    Whole mitochondrial genome capture from faecal samples and museum-preserved specimens2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed)
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