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

• Published in: Nature genetics Vol. 45; no. 7; pp. 776 - 783
• Main Authors: Huang, Yinhua, Li, Yingrui, Burt, David W, Chen, Hualan, Zhang, Yong, Qian, Wubin, Kim, Heebal, Gan, Shangquan, Zhao, Yiqiang, Li, Jianwen, Yi, Kang, Feng, Huapeng, Zhu, Pengyang, Li, Bo, Liu, Qiuyue, Fairley, Suan, Magor, Katharine E, Du, Zhenlin, Hu, Xiaoxiang, Goodman, Laurie, Tafer, Hakim, Vignal, Alain, Lee, Taeheon, Kim, Kyu-Won, Sheng, Zheya, An, Yang, Searle, Steve, Herrero, Javier, Groenen, Martien A M, Crooijmans, Richard P M A, Faraut, Thomas, Cai, Qingle, Webster, Robert G, Aldridge, Jerry R, Warren, Wesley C, Bartschat, Sebastian, Kehr, Stephanie, Marz, Manja, Stadler, Peter F, Smith, Jacqueline, Kraus, Robert H S, Zhao, Yaofeng, Ren, Liming, Fei, Jing, Morisson, Mireille, Kaiser, Pete, Griffin, Darren K, Rao, Man, Pitel, Frederique, Wang, Jun, Li, Ning
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2013; Nature Publishing Group
• Subjects: 631/208/212; a virus; Agriculture; Analysis; Anas platyrhynchos; Animal Genetics and Genomics; Animals; Aquatic birds; Avian influenza virus; Avian influenza viruses; Base Sequence; Biomedicine; Birds; Cancer Research; Chickens - genetics; Chromosomes; defensins; Disease Reservoirs; Disease Vectors; Ducks; Ducks - genetics; Ducks - immunology; Ducks - virology; duplication; expression; Female; Geese - genetics; Gene expression; gene family evolution; Gene Function; Genetic aspects; Genome - physiology; Genomes; Genomics; Health aspects; Host-Pathogen Interactions - genetics; Host-Pathogen Interactions - immunology; Human Genetics; Immunity - genetics; Influenza in Birds - genetics; Influenza in Birds - immunology; Life Sciences; maximum-likelihood; Molecular Sequence Data; phylogenetic trees; Phylogeny; positive selection; protein; Species Specificity; Taeniopygia guttata; Transcriptome - genetics; transmission; Viruses; Wildfowl; Zebra finch; China; duck genome
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.2657

Ning Li and colleagues report the whole-genome sequence of the duck, Anas platyrhynchos , a natural host of avian influenza viruses. They examine host response to infection by comparing the lung transcriptomes of ducks that were infected with influenza A viruses. 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.