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

Yinhua Huang, Dave Burt, Yingrui Li, Hualan Chen, Yong Zhang, Wubin Qian, Heebal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Susan Fairley, Katharine Magor, Zhenlin Du, Xiaoxiang Hu, Laurie GoodmanHakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, Yang An, Steve Searle, Javier Herrero, Martien Am Groenen, Richard Pma Crooijmans, Thomas Faraut, Qingle Cai, Robert Webster, Jerry Aldridge, Wesley C Warren, Sebastian Bartschat, Stephanie Kehr, Manja Marz, Peter Stadler, Jacqueline Smith, Robert Kraus, Yaofeng Zhao, Liming Ren, Jing Fei, Mireille Morisson, Pete Kaiser, Darren K Griffin, Frederique Pitel, Jun Wang, Ning Li

Research output: Contribution to journalArticlepeer-review


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 1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-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.
Original languageEnglish
Pages (from-to)776-U797
JournalNature Genetics
Issue number7
Early online date9 Jun 2013
Publication statusPublished - 2013


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