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

Autor: Mueller RC; Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany.; Department of Biology, University of Konstanz, Konstanz, 78457, Germany., Ellström P; Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, SE-75185, Sweden., Howe K; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Uliano-Silva M; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Kuo RI; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK., Miedzinska K; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK., Warr A; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK., Fedrigo O; Vertebrate Genome Laboratory, The Rockefeller University, New York, 10065, NY., Haase B; Vertebrate Genome Laboratory, The Rockefeller University, New York, 10065, NY., Mountcastle J; Vertebrate Genome Laboratory, The Rockefeller University, New York, 10065, NY., Chow W; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Torrance J; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Wood JMD; Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Järhult JD; Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, SE-75185, Sweden., Naguib MM; Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, 75237, Sweden., Olsen B; Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, SE-75185, Sweden., Jarvis ED; Vertebrate Genome Laboratory and HHMI, The Rockefeller University, New York, 10065, NY., Smith J; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK., Eöry L; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK., Kraus RHS; Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, 78315, Germany.; Department of Biology, University of Konstanz, Konstanz, 78457, Germany.
Jazyk: angličtina
Zdroj: GigaScience [Gigascience] 2021 Dec 20; Vol. 10 (12).
DOI: 10.1093/gigascience/giab081
Abstrakt: 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.
(© The Author(s) 2021. Published by Oxford University Press GigaScience.)
Databáze: MEDLINE
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