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

Publication ,  Journal Article
Mueller, RC; Ellström, P; Howe, K; Uliano-Silva, M; Kuo, RI; Miedzinska, K; Warr, A; Fedrigo, O; Haase, B; Mountcastle, J; Chow, W; Wood, JMD ...
Published in: Gigascience
December 20, 2021

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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Published In

Gigascience

DOI

EISSN

2047-217X

Publication Date

December 20, 2021

Volume

10

Issue

12

Location

United States

Related Subject Headings

  • Transcriptome
  • Male
  • Influenza in Birds
  • Humans
  • Genomics
  • Genome
  • Female
  • Ducks
  • Animals
 

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Mueller, R. C., Ellström, P., Howe, K., Uliano-Silva, M., Kuo, R. I., Miedzinska, K., … Kraus, R. H. S. (2021). A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience, 10(12). https://doi.org/10.1093/gigascience/giab081
Mueller, Ralf C., Patrik Ellström, Kerstin Howe, Marcela Uliano-Silva, Richard I. Kuo, Katarzyna Miedzinska, Amanda Warr, et al. “A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).Gigascience 10, no. 12 (December 20, 2021). https://doi.org/10.1093/gigascience/giab081.
Mueller RC, Ellström P, Howe K, Uliano-Silva M, Kuo RI, Miedzinska K, et al. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience. 2021 Dec 20;10(12).
Mueller, Ralf C., et al. “A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck).Gigascience, vol. 10, no. 12, Dec. 2021. Pubmed, doi:10.1093/gigascience/giab081.
Mueller RC, Ellström P, Howe K, Uliano-Silva M, Kuo RI, Miedzinska K, Warr A, Fedrigo O, Haase B, Mountcastle J, Chow W, Torrance J, Wood JMD, Järhult JD, Naguib MM, Olsen B, Jarvis ED, Smith J, Eöry L, Kraus RHS. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). Gigascience. 2021 Dec 20;10(12).
Journal cover image

Published In

Gigascience

DOI

EISSN

2047-217X

Publication Date

December 20, 2021

Volume

10

Issue

12

Location

United States

Related Subject Headings

  • Transcriptome
  • Male
  • Influenza in Birds
  • Humans
  • Genomics
  • Genome
  • Female
  • Ducks
  • Animals