A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

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2021
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Ellström, Patrik
Howe, Kerstin
Uliano-Silva, Marcela
Kuo, Richard I.
Miedzinska, Katarzyna
Warr, Amanda
Fedrigo, Olivier
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GigaScience. Oxford University Press. 2021, 10(12), giab081. eISSN 2047-217X. Available under: doi: 10.1093/gigascience/giab081
Zusammenfassung

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.
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.
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.

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570 Biowissenschaften, Biologie
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tuftedduck; Aythya fuligula; genome annotation; transcriptome sequencing; Vertebrate Genomes Project; Iso-Seq; Pacific Biosciences; RNA sequencing; smallRNA
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ISO 690MUELLER, Ralf C., Patrik ELLSTRÖM, Kerstin HOWE, Marcela ULIANO-SILVA, Richard I. KUO, Katarzyna MIEDZINSKA, Amanda WARR, Olivier FEDRIGO, Björn OLSEN, Robert KRAUS, 2021. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). In: GigaScience. Oxford University Press. 2021, 10(12), giab081. eISSN 2047-217X. Available under: doi: 10.1093/gigascience/giab081
BibTex
@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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