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

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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.]
    Nature Genetics | Article <ABBR>Open</ABBR>
    <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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  • #2
    Re: Nature Genetics. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

    I saw this only after I had posted to the French thread

    .pdf here: http://www.nature.com/ng/journal/vao...df/ng.2657.pdf

    anas platyrhynchos is the mallard. ---10-week-old female Beijing duck ----
    We were wondering whether the Asian domestic ducks were different
    in that they can get viruses that evolved away from the index,
    which we didn't see in North American mallards.
    Well, it could just be because domestic ducks or commercial ducks
    are not popular in North America.

    A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project



    ftp://ftp.ncbi.nih.gov/genbank/genom...mary_Assembly/

    I didn't find the chromosomes in fasta-format yet
    I'm not sure whether and when they will be available.

    Do I understand correctly, that they have influenza-specific genes, which evolved
    since mallards get influenza ? But that's supposed to be only some thousand years ?!?
    While DNA changes are more slowly. When we dig out the bones of a mallard that died
    >10000 years ago, might that show us whether mallards got flu 10000 years ago ?

    phylo of Eurasian ducks:
    Phylogenetic relationships, demographic history, and geographic distribution of the mtDNA haplotypes of the mallard Anas platyrhynchos were examined in three populations, Indian, Northern European, and Far Eastern. Two divergent haplotype groups, A and B, were found in the Far Eastern population, wh …

    Anas zonorhyncha in Asia, "spot billed duck"

    mitochondrial DNA was published earlier:

    paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586638/



    ================================================== =================


    nonvertebrate euchariotes genomes at genbank

    Alligator mississippiensis
    parrot - Amazona vittata
    mallard - Anas platyrhynchos
    Anolis carolinensis
    Apalone spinifera
    Astyanax mexicanus
    Chelonia mydas
    Chrysemys picta
    rock-pigeon - Columba livia
    Danio rerio
    falcon - Falco cherrug
    falcon - Falco peregrinus
    Halsbandschn&#228;ppe - Ficedula albicollis
    Gadus morhua
    chicken - Gallus gallus
    Fink - Geospiza fortis
    Haplochromis burtoni
    Latimeria chalumnae
    Lepisosteus oculatus
    Maylandia zebra
    turkey - Meleagris gallopavo
    wellensittich - Melopsittacus undulatus
    Neolamprologus brichardi
    Oreochromis niloticus
    Oryzias latipes
    Pelodiscus sinensis
    Petromyzon marinus
    Pseudopodoces humilis
    Pundamilia nyererei
    Taeniopygia guttata
    Takifugu flavidus
    Takifugu rubripes
    Xenopus tropicalis
    Xiphophorus maculatus
    sparrow - Zonotrichia albicollis

    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

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