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

Ralf C Mueller, Patrik Ellström, Kerstin Howe, Marcela Uliano-Silva, Richard I Kuo, Katarzyna Miedzinska, Amanda Warr, Olivier Fedrigo, Bettina Haase, Jacquelyn Mountcastle, William Chow, James Torrance, Jonathan M D Wood, Josef D Järhult, Mahmoud M Naguib, Björn Olsen, Erich D Jarvis, Jacqueline Smith, Lél Eöry, Robert H S Kraus

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Issue number12
Publication statusPublished - 20 Dec 2021


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