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

Nature Genetics

Volumn 45, Issue 7, 2013, Pages 776-783

  Huang, Yinhua ^a,b   Li, Yingrui ^c   Burt, David W ^b   Chen, Hualan ^d   Zhang, Yong ^c   Qian, Wubin ^c   Kim, Heebal ^e   Gan, Shangquan ^a   Zhao, Yiqiang ^a   Li, Jianwen ^c   Yi, Kang ^c   Feng, Huapeng ^d   Zhu, Pengyang ^d   Li, Bo ^c   Liu, Qiuyue ^a   Fairley, Suan ^f   Magor, Katharine E ^g   Du, Zhenlin ^a   Hu, Xiaoxiang ^a   Goodman, Laurie ^c   Tafer, Hakim ^h,i   Vignal, Alain ^j   Lee, Taeheon ^e   Kim, Kyu Won ^k   Sheng, Zheya ^a   An, Yang ^a   Searle, Steve ^f   Herrero, Javier ^l   Groenen, Martien A M ^m   Crooijmans, Richard P M A ^m   Faraut, Thomas ^j   Cai, Qingle ^c   Webster, Robert G ⁿ   Aldridge, Jerry R ⁿ   Warren, Wesley C ^o   Bartschat, Sebastian ^h   Kehr, Stephanie ^h   Marz, Manja ^h   Stadler, Peter F ^h,i   Smith, Jacqueline ^b   Kraus, Robert H S ^m,p   Zhao, Yaofeng ^a   Ren, Liming ^a   Fei, Jing ^a   Morisson, Mireille ^j   Kaiser, Pete ^b   Griffin, Darren K ^q   Rao, Man ^a   Pitel, Frederique ^j   Wang, Jun ^c,r   Li, Ning ^a   more..

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c BGI SHENZHEN   (China)

^d National Key Laboratory of Veterinary Biotechnology   (China)

^e Seoul National University   (South Korea)

^f WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^g UNIVERSITY OF ALBERTA   (Canada)

^h UNIVERSITY OF LEIPZIG   (Germany)

ⁱ UNIVERSITY OF VIENNA   (Austria)

^j CEMAGREF   (France)

^k Seoul National University   (South Korea)

^l EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^m WAGENINGEN UNIVERSITY   (Netherlands)

ⁿ ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^o WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^p SENCKENBERG RESEARCH INSTITUTE   (Germany)

^q UNIVERSITY OF KENT   (United Kingdom)

^r UNIVERSITY OF COPENHAGEN   (Denmark)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVIN; BETA CHEMOKINE; BETA DEFENSIN; BONE MORPHOGENETIC PROTEIN 2; BONE MORPHOGENETIC PROTEIN 5; CHEMOKINE; CXCL3 CHEMOKINE; GAMMA INTERFERON; GROWTH DIFFERENTIATION FACTOR 5; INTERFERON; INTERLEUKIN 10; INTERLEUKIN 2 RECEPTOR; INTERLEUKIN 3 RECEPTOR; INTERLEUKIN 6 RECEPTOR; OSTEOGENIN; TRANSCRIPTOME;

AGE; ANAS PLATYRHYNCHOS; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; AVIAN INFLUENZA; AVIAN INFLUENZA VIRUS; CHICKEN; CONTROLLED STUDY; DUCK; GENE DUPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; HUMAN; INFECTION RESISTANCE; INFLUENZA A (H5N1); INFLUENZA VIRUS A; INFLUENZA VIRUS A H5N1; LUNG; NATURAL HOST; NONHUMAN; PRIORITY JOURNAL; TAENIOPYGIA GUTTATA;

ANIMALS; BASE SEQUENCE; CHICKENS; DISEASE RESERVOIRS; DISEASE VECTORS; DUCKS; FEMALE; GEESE; GENOME; HOST-PATHOGEN INTERACTIONS; IMMUNITY; INFLUENZA IN BIRDS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SPECIES SPECIFICITY; TRANSCRIPTOME;

ANAS; ANAS PLATYRHYNCHOS; AVIAN INFLUENZA VIRUS; INFLUENZA A VIRUS; ORTHOMYXOVIRIDAE; TAENIOPYGIA GUTTATA;

EID: 84879696615     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2657     Document Type: Article

References (45)

1. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716 (2004).
2. Warren, W.C. et al. The genome of a songbird. Nature 464, 757-762 (2010).
3. Dalloul, R.A. et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 8, e1000475 (2010).
4. Hackett, S.J. et al. A phylogenomic study of birds reveals their evolutionary history. Science 320, 1763-1768 (2008).
5. Olsen, B. et al. Global patterns of influenza A virus in wild birds. Science 312, 384-388 (2006).
6. Wilcox, B.R. et al. Influenza-A viruses in ducks in northwestern Minnesota: fine scale spatial and temporal variation in prevalence and subtype diversity. PLoS ONE 6, e24010 (2011).
7. Munster, V.J. et al. Spatial, temporal, and species variation in prevalence of influenza A viruses in wild migratory birds. PLoS Pathog. 3, e61 (2007).
8. Sturm-Ramirez, K.M. et al. Are ducks contributing to the endemicity of highly pathogenic H5N1 influenza virus in Asia? J. Virol. 79, 11269-11279 (2005).
9. Imai, M. et al. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmissio to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486, 420-428 (2012).
10. Lin, Y.P. et al. Avian-to-human transmission of H9N2 subtype influenza A viruses: relationship between H9N2 and H5N1 human isolates. Proc. Natl. Acad. Sci. USA 97, 9654-9658 (2000).
11. Belser, J.A. et al. Contemporary North American influenza H7 viruses possess human receptor specificity: implications for virus transmissibility. Proc. Natl. Acad. Sci. USA 105, 7558-7563 (2008).
12. Butt, K.M. et al. Human infection with an avian H9N2 influenza A virus in Hong Kong in 2003. J. Clin. Microbiol. 43, 5760-5767 (2005).
13. Song, J. et al. The PA protein directly contribute to the virulence of H5N1 avian influenza viruses in domestic ducks. J. Virol. 85, 2180-2188 (2011).
14. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
15. Huang, Y. et al. A genetic and cytogenetic map for the duck (Anas platyrhynchos). Genetics 173, 287-296 (2006).
16. Skinner, B.M. et al. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics 10, 357 (2009).
17. Huang, Y. et al. Molecular evolution of the vertebrate TLR1 gene family-a complex history of gene duplication, gene conversion, positive selection and co-evolution. BMC Evol. Biol. 11, 149 (2011).
18. Courcelle, E. et al. Narcisse: a mirror view of conserved syntenies. Nucleic Acids Res. 36, D485-D490 (2008).
19. Salamov, A.A. & Solovyev, V.V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516-522 (2000).
20. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl. 2), ii215-ii225 (2003).
21. Hahn, M.W., De Bie, T., Stajich, J.E., Nguyen, C. & Cristianini, N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15, 1153-1160 (2005).
22. Hahn, M.W., Han, M.V. & Han, S.G. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3, e197 (2007).
23. Hahn, M.W., Demuth, J.P. & Han, S.G. Accelerated rate of gene gain and loss in primates. Genetics 177, 1941-1949 (2007).
24. Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580 (2006).
25. Xiao, Y. et al. A genome-wide screen identifies a single β-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins. BMC Genomics 5, 56 (2004).
26. Hellgren, O. & Ekblom, R. Evolution of a cluster of innate immune genes (β-defensins) along the ancestral lines of chicken and zebra finch. Immunome Res. 6, 3 (2010).
27. Letunic, I., Doerks, T. & Bork, P. SMART 6: recent updates and new developments. Nucleic Acids Res. 37, D229-D232 (2009).
28. Bas, A. et al. Butyrophilin-like 1 encodes an enterocyte protein that selectively regulates functional interactions with T lymphocytes. Proc. Natl. Acad. Sci. USA 108, 4376-4381 (2011).
29. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
30. Nam, K. et al. Molecular evolution of genes in avian genomes. Genome Biol. 11, R68 (2010).
31. Schneider, A. et al. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol. Evol. 1, 114-118 (2009).
32. Fletcher, W. & Yang, Z. The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol. Biol. Evol. 27, 2257-2267 (2010).
33. Rothenburg, S., Seo, E.J., Gibbs, J.S., Dever, T.E. & Dittmar, K. Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors. Nat. Struct. Mol. Biol. 16, 63-70 (2009).
34. Sawyer, S.L., Wu, L.I., Emerman, M. & Malik, H.S. Positive selection of primate TRIM5α identifies a critical species-specific retroviral restriction domain. Proc. Natl. Acad. Sci. USA 102, 2832-2837 (2005).
35. Barber, M.R., Aldridge, J.R. Jr., Webster, R.G. & Magor, K.E. Association of RIG-I with innate immunity of ducks to influenza. Proc. Natl. Acad. Sci. USA 107, 5913-5918 (2010).
36. Pichlmair, A. et al. IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA. Nat. Immunol. 12, 624-630 (2011).
37. Everitt, A.R. et al. IFITM3 restricts the morbidity and mortality associated with influenza. Nature 484, 519-523 (2012).
38. Chong, K.T., Thangavel, R.R. & Tang, X. Enhanced expression of murine β-defensins (MBD-1, -2,- 3, and -4) in upper and lower airway mucosa of influenza virus infected mice. Virology 380, 136-143 (2008).
39. Doss, M. et al. Interactions of α-, β-, and θ-defensins with influenza A virus and surfactant protein D. J. Immunol. 182, 7878-7887 (2009).
40. Nguyen, T., Liu, X.K., Zhang, Y. & Dong, C. BTNL2, a butyrophilin-like molecule that functions to inhibit T cell activation. J. Immunol. 176, 7354-7360 (2006).
41. Vilella, A.J. et al. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19, 327-335 (2009).
42. Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704 (2003).
43. Chen, H. H5N1 avian influenza in China. Sci. China C Life Sci. 52, 419-427 (2009).
44. Audic, S. & Claverie, J.M. The significance of digital gene expression profiles. Genome Res. 7, 986-995 (1997).
45. Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165-1188 (2001). of China Science and Technology 948 Program