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; Susan 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

doi:10.1038/ng.2657

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, Susan Fairley, Katharine E Magor, Zhenlin Du, Xiaoxiang Hu, Laurie GoodmanHakim 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

Applied Medicine

Research output: Contribution to journal › Article › peer-review

279 Citations (Scopus)

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.

Original language	English
Pages (from-to)	776-783
Number of pages	8
Journal	Nature Genetics
Volume	45
Issue number	7
Early online date	9 Jun 2013
DOIs	https://doi.org/10.1038/ng.2657
Publication status	Published - Jul 2013

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10.1038/ng.2657Licence: CC BY-NC-SA

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Huang, Y, Li, Y, Burt, DW, Chen, H, Zhang, Y, Qian, W, Kim, H, Gan, S, Zhao, Y, Li, J, Yi, K, Feng, H, Zhu, P, Li, B, Liu, Q, Fairley, S, Magor, KE, Du, Z, Hu, X, Goodman, L, Tafer, H, Vignal, A, Lee, T, Kim, K-W, Sheng, Z, An, Y, Searle, S, Herrero, J, Groenen, MAM, Crooijmans, RPMA, Faraut, T, Cai, Q, Webster, RG, Aldridge, JR, Warren, WC, Bartschat, S, Kehr, S, Marz, M, Stadler, PF, Smith, J, Kraus, RHS, Zhao, Y, Ren, L, Fei, J, Morisson, M, Kaiser, P, Griffin, DK, Rao, M, Pitel, F, Wang, J & Li, N 2013, 'The duck genome and transcriptome provide insight into an avian influenza virus reservoir species', Nature Genetics, vol. 45, no. 7, pp. 776-783. https://doi.org/10.1038/ng.2657

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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.",

author = "Yinhua Huang and Yingrui Li and Burt, {David W} and Hualan Chen and Yong Zhang and Wubin Qian and Heebal Kim and Shangquan Gan and Yiqiang Zhao and Jianwen Li and Kang Yi and Huapeng Feng and Pengyang Zhu and Bo Li and Qiuyue Liu and Susan Fairley and Magor, {Katharine E} and Zhenlin Du and Xiaoxiang Hu and Laurie Goodman and Hakim Tafer and Alain Vignal and Taeheon Lee and Kyu-Won Kim and Zheya Sheng and Yang An and Steve Searle and Javier Herrero and Groenen, {Martien A M} and Crooijmans, {Richard P M A} and Thomas Faraut and Qingle Cai and Webster, {Robert G} and Aldridge, {Jerry R} and Warren, {Wesley C} and Sebastian Bartschat and Stephanie Kehr and Manja Marz and Stadler, {Peter F} and Jacqueline Smith and Kraus, {Robert H S} and Yaofeng Zhao and Liming Ren and Jing Fei and Mireille Morisson and Pete Kaiser and Griffin, {Darren K} and Man Rao and Frederique Pitel and Jun Wang and Ning Li",

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AU - Huang, Yinhua

AU - Li, Yingrui

AU - Burt, David W

AU - Chen, Hualan

AU - Zhang, Yong

AU - Qian, Wubin

AU - Kim, Heebal

AU - Gan, Shangquan

AU - Zhao, Yiqiang

AU - Li, Jianwen

AU - Yi, Kang

AU - Feng, Huapeng

AU - Zhu, Pengyang

AU - Li, Bo

AU - Liu, Qiuyue

AU - Fairley, Susan

AU - Magor, Katharine E

AU - Du, Zhenlin

AU - Hu, Xiaoxiang

AU - Goodman, Laurie

AU - Tafer, Hakim

AU - Vignal, Alain

AU - Lee, Taeheon

AU - Kim, Kyu-Won

AU - Sheng, Zheya

AU - An, Yang

AU - Searle, Steve

AU - Herrero, Javier

AU - Groenen, Martien A M

AU - Crooijmans, Richard P M A

AU - Faraut, Thomas

AU - Cai, Qingle

AU - Webster, Robert G

AU - Aldridge, Jerry R

AU - Warren, Wesley C

AU - Bartschat, Sebastian

AU - Kehr, Stephanie

AU - Marz, Manja

AU - Stadler, Peter F

AU - Smith, Jacqueline

AU - Kraus, Robert H S

AU - Zhao, Yaofeng

AU - Ren, Liming

AU - Fei, Jing

AU - Morisson, Mireille

AU - Kaiser, Pete

AU - Griffin, Darren K

AU - Rao, Man

AU - Pitel, Frederique

AU - Wang, Jun

AU - Li, Ning

PY - 2013/7

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N2 - 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.

AB - 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.

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VL - 45

SP - 776

EP - 783

JO - Nature Genetics

JF - Nature Genetics

IS - 7

ER -

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

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