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Nat Genet. 2013 Jul;45(7):776-783. doi: 10.1038/ng.2657. Epub 2013 Jun 9.

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.

Author information

1
State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
2
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
3
BGI-Shenzhen, Shenzhen, China.
4
National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.
5
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
6
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
7
Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
8
Department of Computer Science, University of Leipzig, Leipzig, Germany.
9
Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.
10
Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
11
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.
12
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
13
Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
14
Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
15
The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
16
Resource Ecology Group, Wageningen University, Wageningen, The Netherlands.
17
Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany.
18
Genetics School of Biosciences, University of Kent, Kent, UK.
19
Department of Biology, University of Copenhagen, Copenhagen, Denmark.
#
Contributed equally

Abstract

The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its β-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.

PMID:
23749191
PMCID:
PMC4003391
DOI:
10.1038/ng.2657
[Indexed for MEDLINE]
Free PMC Article

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