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

Nature Genetics

Year published:(2013)

Received：16 December 2012

Accepted：08 May 2013

Published online：09 June 2013

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.

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2657.html#ref15

Affiliations

1. State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.

   • Yinhua Huang,
   • Shangquan Gan,
   • Yiqiang Zhao,
   • Qiuyue Liu,
   • Zhenlin Du,
   • Xiaoxiang Hu,
   • Zheya Sheng,
   • Yang An,
   • Yaofeng Zhao,
   • Liming Ren,
   • Jing Fei,
   • Man Rao &
   • Ning Li

2. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.

   • Yinhua Huang,
   • David W Burt,
   • Jacqueline Smith &
   • Pete Kaiser

3. BGI-Shenzhen, Shenzhen, China.

   • Yingrui Li,
   • Yong Zhang,
   • Wubin Qian,
   • Jianwen Li,
   • Kang Yi,
   • Bo Li,
   • Laurie Goodman,
   • Qingle Cai &
   • Jun Wang

4. National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.

   • Hualan Chen,
   • Huapeng Feng &
   • Pengyang Zhu

5. Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

   • Heebal Kim &
   • Taeheon Lee

6. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

   • Suan Fairley &
   • Steve Searle

7. Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.

   • Katharine E Magor

8. Department of Computer Science, University of Leipzig, Leipzig, Germany.

   • Hakim Tafer,
   • Sebastian Bartschat,
   • Stephanie Kehr,
   • Manja Marz &
   • Peter F Stadler

9. Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.

   • Hakim Tafer &
   • Peter F Stadler

10. Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.

    • Alain Vignal,
    • Thomas Faraut,
    • Mireille Morisson &
    • Frederique Pitel

11. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.

    • Kyu-Won Kim

12. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Javier Herrero

13. Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.

    • Martien A M Groenen &
    • Richard P M A Crooijmans

14. Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Robert G Webster &
    • Jerry R Aldridge

15. The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

    • Wesley C Warren

16. Resource Ecology Group, Wageningen University, Wageningen, The Netherlands.

    • Robert H S Kraus

17. Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany.

    • Robert H S Kraus

18. Genetics School of Biosciences, University of Kent, Kent, UK.

    • Darren K Griffin

19. Department of Biology, University of Copenhagen, Copenhagen, Denmark.

    • Jun Wang