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

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      1 , 2 , 3 , 2 , 4 , 3 , 3 , 5 , 1 , 1 , 3 , 3 , 4 , 4 , 3 , 1 , 6 , 7 , 1 , 1 , 3 , 8 , 9 , 10 , 5 , 11 , 1 , 1 , 6 , 12 , 13 , 13 , 10 , 3 , 14 , 14 , 15 , 8 , 8 , 8 , 8 , 9 , 2 , 16 , 17 , 1 , 1 , 1 , 10 , 2 , 18 , 1 , 10 , 3 , 19 , 1
      Nature genetics

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          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.

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          Most cited references26

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          Ab initio gene finding in Drosophila genomic DNA.

          Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.
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            SMART 6: recent updates and new developments

            Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains manually curated models for 784 protein domains. Recent developments were focused on further data integration and improving user friendliness. The underlying protein database based on completely sequenced genomes was greatly expanded and now includes 630 species, compared to 191 in the previous release. As an initial step towards integrating information on biological pathways into SMART, our domain annotations were extended with data on metabolic pathways and links to several pathways resources. The interaction network view was completely redesigned and is now available for more than 2 million proteins. In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service.
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              IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA.

              Antiviral innate immunity relies on the recognition of microbial structures. One such structure is viral RNA that carries a triphosphate group on its 5' terminus (PPP-RNA). By an affinity proteomics approach with PPP-RNA as the 'bait', we found that the antiviral protein IFIT1 (interferon-induced protein with tetratricopeptide repeats 1) mediated binding of a larger protein complex containing other IFIT family members. IFIT1 bound PPP-RNA with nanomolar affinity and required the arginine at position 187 in a highly charged carboxy-terminal groove of the protein. In the absence of IFIT1, the growth and pathogenicity of viruses containing PPP-RNA was much greater. In contrast, IFIT proteins were dispensable for the clearance of pathogens that did not generate PPP-RNA. On the basis of this specificity and the great abundance of IFIT proteins after infection, we propose that the IFIT complex antagonizes viruses by sequestering specific viral nucleic acids.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nat. Genet.
                Nature genetics
                1061-4036
                1546-1718
                22 April 2014
                09 June 2013
                July 2013
                29 April 2014
                : 45
                : 7
                : 776-783
                Affiliations
                [1 ]State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.
                [2 ]The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
                [3 ]BGI-Shenzhen, Shenzhen, China.
                [4 ]National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China.
                [5 ]Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
                [6 ]Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
                [7 ]Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
                [8 ]Department of Computer Science, University of Leipzig, Leipzig, Germany.
                [9 ]Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.
                [10 ]Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France.
                [11 ]Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.
                [12 ]European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
                [13 ]Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands.
                [14 ]Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
                [15 ]The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
                [16 ]Resource Ecology Group, Wageningen University, Wageningen, The Netherlands.
                [17 ]Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany.
                [18 ]Genetics School of Biosciences, University of Kent, Kent, UK.
                [19 ]Department of Biology, University of Copenhagen, Copenhagen, Denmark.
                Author notes
                Correspondence should be addressed to J.W. ( wangj@ 123456genomics.org.cn ) or N.L. ( ninglcau@ 123456cau.edu.cn )

                AUTHOR 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.

                Article
                EMS58073
                10.1038/ng.2657
                4003391
                23749191
                3f16e53d-b515-4b56-9aea-f8f79bd77909
                © 2013 Nature America, Inc. All rights reserved.

                This work is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/

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