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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
GigaScience, Volume 10, No. 12, Article giab081, Year 2021
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Description
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. © 2021 The Author(s).
Authors & Co-Authors
Ellström, Patrik
Sweden, Uppsala
Uppsala Universitet
Howe, Kerstin
United Kingdom, Hinxton
Wellcome Sanger Institute
Uliano-Silva, Marcela
United Kingdom, Hinxton
Wellcome Sanger Institute
Kuo, Richard I.
United Kingdom, Edinburgh
The University of Edinburgh
Miedzinska, Katarzyna
United Kingdom, Edinburgh
The University of Edinburgh
Fédrigo, Olivier D.
United States, New York
Rockefeller University
Mountcastle, Jacquelyn
United States, New York
Rockefeller University
Chow, William
United Kingdom, Hinxton
Wellcome Sanger Institute
Torrance, James W.
United Kingdom, Hinxton
Wellcome Sanger Institute
Wood, Jonathan M.D.
United Kingdom, Hinxton
Wellcome Sanger Institute
Järhult, Josef D.
Sweden, Uppsala
Uppsala Universitet
Naguib, M. M.
Sweden, Uppsala
Uppsala Universitet
Olsen, Björn
Sweden, Uppsala
Uppsala Universitet
Jarvis, Erich D.
United States, New York
Rockefeller University
Smith, Jacqueline Gustav
United Kingdom, Edinburgh
The University of Edinburgh
Eöry, Lél A.
United Kingdom, Edinburgh
The University of Edinburgh
Kraus, Robert H. S.
Germany, Radolfzell
Max Planck Institute of Animal Behavior
Germany, Konstanz
Universität Konstanz
Statistics
Citations: 3
Authors: 17
Affiliations: 6
Identifiers
Doi:
10.1093/gigascience/giab081
ISSN:
2047217X
Research Areas
Genetics And Genomics