@article{Mueller2021-12-20highq-56515,
  year={2021},
  doi={10.1093/gigascience/giab081},
  title={A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)},
  number={12},
  volume={10},
  journal={GigaScience},
  author={Mueller, Ralf C. and Ellström, Patrik and Howe, Kerstin and Uliano-Silva, Marcela and Kuo, Richard I. and Miedzinska, Katarzyna and Warr, Amanda and Fedrigo, Olivier and Olsen, Björn and Kraus, Robert},
  note={Article Number: giab081}
}

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    <dc:creator>Miedzinska, Katarzyna</dc:creator>
    <dc:contributor>Miedzinska, Katarzyna</dc:contributor>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-02-10T13:13:02Z</dcterms:available>
    <dc:contributor>Howe, Kerstin</dc:contributor>
    <dc:contributor>Olsen, Björn</dc:contributor>
    <dc:contributor>Kuo, Richard I.</dc:contributor>
    <dc:rights>Attribution 4.0 International</dc:rights>
    <dc:creator>Howe, Kerstin</dc:creator>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-02-10T13:13:02Z</dc:date>
    <dc:contributor>Uliano-Silva, Marcela</dc:contributor>
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    <dc:contributor>Warr, Amanda</dc:contributor>
    <dcterms:abstract xml:lang="eng">Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.&lt;br /&gt;Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.&lt;br /&gt;Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.</dcterms:abstract>
    <dc:language>eng</dc:language>
    <dc:creator>Warr, Amanda</dc:creator>
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    <dc:creator>Kuo, Richard I.</dc:creator>
    <dcterms:issued>2021-12-20</dcterms:issued>
    <dc:creator>Uliano-Silva, Marcela</dc:creator>
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    <dc:creator>Fedrigo, Olivier</dc:creator>
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    <dc:contributor>Fedrigo, Olivier</dc:contributor>
    <dcterms:title>A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)</dcterms:title>
    <dc:creator>Olsen, Björn</dc:creator>
    <dc:contributor>Ellström, Patrik</dc:contributor>
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    <dc:contributor>Mueller, Ralf C.</dc:contributor>
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    <dc:creator>Kraus, Robert</dc:creator>
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    <dc:creator>Ellström, Patrik</dc:creator>
    <dc:contributor>Kraus, Robert</dc:contributor>
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