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Nature Genetics. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
[Source: Nature Genetics, full open access document: (LINK). Abstract, edited.]
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Nature Genetics | Article <ABBR>Open</ABBR>
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<ABBR></ABBR>The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang, Wubin Qian, Heebal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Suan Fairley, Katharine E Magor, Zhenlin Du, Xiaoxiang Hu, Laurie Goodman, Hakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, Yang An, Steve Searle, Javier Herrero, Martien A M Groenen, Richard P M A Crooijmans, Thomas Faraut, Qingle Cai, Robert G Webster, Jerry R Aldridge, Wesley C Warren, Sebastian Bartschat, Stephanie Kehr, Manja Marz, Peter F Stadler, Jacqueline Smith , Robert H S Kraus, Yaofeng Zhao, Liming Ren, Jing Fei, Mireille Morisson, Pete Kaiser, Darren K Griffin, Man Rao, Frederique Pitel, Jun Wang & Ning Li et al.
Journal name: Nature Genetics - Year published: (2013) DOI: doi:10.1038/ng.2657
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.
Contributions
N.L., J.W., Y.H. and D.W.B. organized the committee for the duck genome sequencing project. N.L., J.W., Y.H., X.H., L.R. and J.F. designed the duck genome sequence project. J.W., W.Q., Y.L. and Y. Zhang sequenced and assembled the duck genome. W.Q., Y.H., A.V. and T.F. assessed the quality of the duck genome. J.L., W.Q., S.F., Y.H., B.L., A.V., S.S., Yiqiang Zhao, Z.D., Q.C., H.T., S.B., S.K., M. Marz, M. Morisson, M.R., F.P. and P.F.S. performed gene prediction and annotation. D.W.B., H.K., Y.H., B.L., J.H., T.L., K.-W.K., J.S. and D.K.G. performed gene evolutionary analysis. Y.H., W.Q., D.W.B., Q.L., Z.D., Z.S., Y.A. and P.K. detected expansion and contraction of immune-related genes. Y.H., N.L., S.G., W.Q., Z.S. and Y.A. analyzed β-defensin and immunoglobulin genes. Y.H., N.L., H.C., K.Y., H.F., P.Z., D.W.B., K.E.M., R.G.W., J.R.A. and W.C.W. characterized the immune-related gene response to avian influenza viruses. Y.H. and W.Q. wrote the manuscript. N.L., Y.H., D.W.B., L.G., J.W., M.A.M.G., R.P.M.A.C., Yaofeng Zhao, R.H.S.K., A.V., K.E.M. and J.S. revised the manuscript.
Competing financial interests
The authors declare no competing financial interests.
Corresponding authors
Correspondence to: Jun Wang or Ning Li
-<ABBR></ABBR>
<ABBR></ABBR>The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang, Wubin Qian, Heebal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Suan Fairley, Katharine E Magor, Zhenlin Du, Xiaoxiang Hu, Laurie Goodman, Hakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, Yang An, Steve Searle, Javier Herrero, Martien A M Groenen, Richard P M A Crooijmans, Thomas Faraut, Qingle Cai, Robert G Webster, Jerry R Aldridge, Wesley C Warren, Sebastian Bartschat, Stephanie Kehr, Manja Marz, Peter F Stadler, Jacqueline Smith , Robert H S Kraus, Yaofeng Zhao, Liming Ren, Jing Fei, Mireille Morisson, Pete Kaiser, Darren K Griffin, Man Rao, Frederique Pitel, Jun Wang & Ning Li et al.
Journal name: Nature Genetics - Year published: (2013) DOI: doi:10.1038/ng.2657
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.
Contributions
N.L., J.W., Y.H. and D.W.B. organized the committee for the duck genome sequencing project. N.L., J.W., Y.H., X.H., L.R. and J.F. designed the duck genome sequence project. J.W., W.Q., Y.L. and Y. Zhang sequenced and assembled the duck genome. W.Q., Y.H., A.V. and T.F. assessed the quality of the duck genome. J.L., W.Q., S.F., Y.H., B.L., A.V., S.S., Yiqiang Zhao, Z.D., Q.C., H.T., S.B., S.K., M. Marz, M. Morisson, M.R., F.P. and P.F.S. performed gene prediction and annotation. D.W.B., H.K., Y.H., B.L., J.H., T.L., K.-W.K., J.S. and D.K.G. performed gene evolutionary analysis. Y.H., W.Q., D.W.B., Q.L., Z.D., Z.S., Y.A. and P.K. detected expansion and contraction of immune-related genes. Y.H., N.L., S.G., W.Q., Z.S. and Y.A. analyzed β-defensin and immunoglobulin genes. Y.H., N.L., H.C., K.Y., H.F., P.Z., D.W.B., K.E.M., R.G.W., J.R.A. and W.C.W. characterized the immune-related gene response to avian influenza viruses. Y.H. and W.Q. wrote the manuscript. N.L., Y.H., D.W.B., L.G., J.W., M.A.M.G., R.P.M.A.C., Yaofeng Zhao, R.H.S.K., A.V., K.E.M. and J.S. revised the manuscript.
Competing financial interests
The authors declare no competing financial interests.
Corresponding authors
Correspondence to: Jun Wang or Ning Li
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