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A high-quality geno...
A high-quality genome and comparison of short-versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
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- Mueller, Ralf C. (författare)
- Max Planck Inst Anim Behavior, Dept Radolfzell, D-78315 Radolfzell am Bodensee, Germany.;Univ Konstanz, Dept Biol, D-78457 Constance, Germany.
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- Ellström, Patrik (författare)
- Uppsala universitet,Infektionsmedicin
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- Howe, Kerstin (författare)
- Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
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- Uliano-Silva, Marcela (författare)
- Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
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- Kuo, Richard I. (författare)
- Univ Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
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- Miedzinska, Katarzyna (författare)
- Univ Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
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- Warr, Amanda (författare)
- Univ Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
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- Fedrigo, Olivier (författare)
- Rockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
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- Haase, Bettina (författare)
- Rockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
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- Mountcastle, Jacquelyn (författare)
- Rockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
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- Chow, William (författare)
- Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
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- Torrance, James (författare)
- Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
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- Wood, Jonathan M. D. (författare)
- Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
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- Järhult, Josef D., 1975- (författare)
- Uppsala universitet,Infektionsmedicin
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- Naguib, Mahmoud (författare)
- Uppsala universitet,Infektionsmedicin
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- Olsen, Björn (författare)
- Uppsala universitet,Infektionsmedicin
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Jarvis, Erich D. (författare)
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- Smith, Jacqueline (författare)
- Univ Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
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- Eory, Lel (författare)
- Univ Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
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- Kraus, Robert H. S. (författare)
- Max Planck Inst Anim Behavior, Dept Radolfzell, D-78315 Radolfzell am Bodensee, Germany.;Univ Konstanz, Dept Biol, D-78457 Constance, Germany.
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Max Planck Inst Anim Behavior, Dept Radolfzell, D-78315 Radolfzell am Bodensee, Germany;Univ Konstanz, Dept Biol, D-78457 Constance, Germany. Infektionsmedicin (creator_code:org_t)
- 2021-12-20
- 2021
- Engelska.
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 10:12
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- tufted duck
- Aythyafuligula
- genome annotation
- transcriptome sequencing
- Vertebrate Genomes Project
- Iso-Seq
- Pacific Biosciences
- RNA sequencing
- small RNA
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
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Mueller, Ralf C.
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Ellström, Patrik
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Howe, Kerstin
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Uliano-Silva, Ma ...
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Kuo, Richard I.
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Miedzinska, Kata ...
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visa fler...
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Warr, Amanda
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Fedrigo, Olivier
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Haase, Bettina
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Mountcastle, Jac ...
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Chow, William
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Torrance, James
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Wood, Jonathan M ...
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Järhult, Josef D ...
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Naguib, Mahmoud
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Olsen, Björn
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Jarvis, Erich D.
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Smith, Jacquelin ...
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Eory, Lel
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Kraus, Robert H. ...
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visa färre...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Genetik
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Uppsala universitet