title: The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.
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.
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.|The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
authors.forename: Yinhua
authors.initials: Y
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.affiliation: National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.
authors.forename: Hualan
authors.initials: H
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Wubin
authors.initials: W
authors.lastname: Qian
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Shangquan
authors.initials: S
authors.lastname: Gan
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Yiqiang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jianwen
authors.initials: J
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Kang
authors.initials: K
authors.lastname: Yi
authors.affiliation: National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.
authors.forename: Huapeng
authors.initials: H
authors.lastname: Feng
authors.affiliation: National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.
authors.forename: Pengyang
authors.initials: P
authors.lastname: Zhu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Qiuyue
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Suan
authors.initials: S
authors.lastname: Fairley
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Katharine E
authors.initials: KE
authors.lastname: Magor
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Zhenlin
authors.initials: Z
authors.lastname: Du
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Xiaoxiang
authors.initials: X
authors.lastname: Hu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Laurie
authors.initials: L
authors.lastname: Goodman
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany.|Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.affiliation: Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Vignal
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
authors.forename: Taeheon
authors.initials: T
authors.lastname: Lee
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.
authors.forename: Kyu-Won
authors.initials: KW
authors.lastname: Kim
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Zheya
authors.initials: Z
authors.lastname: Sheng
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: An
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Steve
authors.initials: S
authors.lastname: Searle
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Herrero
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
authors.forename: Martien A M
authors.initials: MAM
authors.lastname: Groenen
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
authors.forename: Richard P M A
authors.initials: RPMA
authors.lastname: Crooijmans
authors.affiliation: Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Faraut
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qingle
authors.initials: Q
authors.lastname: Cai
authors.affiliation: Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Webster
authors.affiliation: Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
authors.forename: Jerry R
authors.initials: JR
authors.lastname: Aldridge
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bartschat
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kehr
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.affiliation: Department of Computer Science, University of Leipzig, Leipzig, Germany.|Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Smith
authors.affiliation: Resource Ecology Group, Wageningen University, Wageningen, The Netherlands.|Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany.
authors.forename: Robert H S
authors.initials: RHS
authors.lastname: Kraus
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Yaofeng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Liming
authors.initials: L
authors.lastname: Ren
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Fei
authors.affiliation: Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Morisson
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
authors.forename: Pete
authors.initials: P
authors.lastname: Kaiser
authors.affiliation: Genetics School of Biosciences, University of Kent, Kent, UK.
authors.forename: Darren K
authors.initials: DK
authors.lastname: Griffin
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Man
authors.initials: M
authors.lastname: Rao
authors.affiliation: Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
authors.forename: Frederique
authors.initials: F
authors.lastname: Pitel
authors.affiliation: BGI-Shenzhen, Shenzhen, China.|Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
mesh_terms: D000818:Animals; D001483:Base Sequence; D002645:Chickens / Q000235:genetics; D004197:Disease Reservoirs; D004199:Disease Vectors; D004372:Ducks / Q000235:genetics* / Q000276:immunology / Q000821:virology*; D005260:Female; D005777:Geese / Q000235:genetics; D016678:Genome / Q000502:physiology; D054884:Host-Pathogen Interactions / Q000235:genetics / Q000276:immunology; D007109:Immunity / Q000235:genetics; D005585:Influenza in Birds / Q000235:genetics* / Q000276:immunology; D008969:Molecular Sequence Data; D010802:Phylogeny; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*