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A high-quality geno...
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Mueller, Ralf C.Max Planck Inst Anim Behavior, Dept Radolfzell, D-78315 Radolfzell am Bodensee, Germany.;Univ Konstanz, Dept Biol, D-78457 Constance, Germany.
(författare)
A high-quality genome and comparison of short-versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
- Artikel/kapitelEngelska2021
Förlag, utgivningsår, omfång ...
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2021-12-20
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Oxford University Press,2021
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electronicrdacarrier
Nummerbeteckningar
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LIBRIS-ID:oai:DiVA.org:uu-467415
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-467415URI
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https://doi.org/10.1093/gigascience/giab081DOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:art swepub-publicationtype
Anmärkningar
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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 och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Ellström, PatrikUppsala universitet,Infektionsmedicin(Swepub:uu)patel687
(författare)
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Howe, KerstinWellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
(författare)
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Uliano-Silva, MarcelaWellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
(författare)
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Kuo, Richard I.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.
(författare)
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Miedzinska, KatarzynaUniv Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
(författare)
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Warr, AmandaUniv Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
(författare)
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Fedrigo, OlivierRockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
(författare)
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Haase, BettinaRockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
(författare)
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Mountcastle, JacquelynRockefeller Univ, Vertebrate Genom Lab, New York, NY 10065 USA.
(författare)
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Chow, WilliamWellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
(författare)
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Torrance, JamesWellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
(författare)
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Wood, Jonathan M. D.Wellcome Sanger Inst, Tree Life, Cambridge CB101SA, England.
(författare)
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Järhult, Josef D.,1975-Uppsala universitet,Infektionsmedicin(Swepub:uu)josja939
(författare)
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Naguib, MahmoudUppsala universitet,Infektionsmedicin(Swepub:uu)mahna768
(författare)
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Olsen, BjörnUppsala universitet,Infektionsmedicin(Swepub:uu)bjool781
(författare)
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Jarvis, Erich D.
(författare)
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Smith, JacquelineUniv Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
(författare)
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Eory, LelUniv Edinburgh, Roslin Inst, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush, Roslin EH25 9RG, Midlothian, Scotland.
(författare)
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Kraus, Robert H. S.Max Planck Inst Anim Behavior, Dept Radolfzell, D-78315 Radolfzell am Bodensee, Germany.;Univ Konstanz, Dept Biol, D-78457 Constance, Germany.
(författare)
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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)
Sammanhörande titlar
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Ingår i:GigaScience: Oxford University Press10:122047-217X
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- 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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