Advertisement
Research Article

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

  • Rami A. Dalloul equal contributor,

    equal contributor Contributed equally to this work with: Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin

    Affiliation: Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Julie A. Long equal contributor,

    equal contributor Contributed equally to this work with: Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin

    Affiliation: Animal Biosciences and Biotechnology Laboratory, USDA Agricultural Research Service, Beltsville, Maryland, United States of America

    X
  • Aleksey V. Zimin equal contributor,

    equal contributor Contributed equally to this work with: Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin

    Affiliation: Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America

    X
  • Luqman Aslam,

    Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands

    X
  • Kathryn Beal,

    Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Le Ann Blomberg,

    Affiliation: Animal Biosciences and Biotechnology Laboratory, USDA Agricultural Research Service, Beltsville, Maryland, United States of America

    X
  • Pascal Bouffard,

    Affiliation: Roche Applied Science, Indianapolis, Indiana, United States of America

    X
  • David W. Burt,

    Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom

    X
  • Oswald Crasta,

    Affiliations: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America, Chromatin Inc., Champaign, Illinois, United States of America

    X
  • Richard P. M. A. Crooijmans,

    Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands

    X
  • Kristal Cooper,

    Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Roger A. Coulombe,

    Affiliation: Department of Veterinary Sciences, Utah State University, Logan, Utah, United States of America

    X
  • Supriyo De,

    Affiliation: Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America

    X
  • Mary E. Delany,

    Affiliation: Department of Animal Science, University of California, Davis, California, United States of America

    X
  • Jerry B. Dodgson,

    Affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America

    X
  • Jennifer J. Dong,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Clive Evans,

    Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Karin M. Frederickson,

    Affiliation: Roche Applied Science, Indianapolis, Indiana, United States of America

    X
  • Paul Flicek,

    Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Liliana Florea,

    Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

    X
  • Otto Folkerts,

    Affiliations: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America, Chromatin Inc., Champaign, Illinois, United States of America

    X
  • Martien A. M. Groenen,

    Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands

    X
  • Tim T. Harkins,

    Affiliation: Roche Applied Science, Indianapolis, Indiana, United States of America

    X
  • Javier Herrero,

    Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Steve Hoffmann,

    Affiliations: Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany, LIFE Project, University of Leipzig, Leipzig, Germany

    X
  • Hendrik-Jan Megens,

    Affiliation: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands

    X
  • Andrew Jiang,

    Affiliation: Department of Animal Science, University of California, Davis, California, United States of America

    X
  • Pieter de Jong,

    Affiliation: Children's Hospital and Research Center at Oakland, Oakland, California, United States of America

    X
  • Pete Kaiser,

    Affiliation: Institute for Animal Health, Compton, Berkshire, United Kingdom

    X
  • Heebal Kim,

    Affiliation: Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea

    X
  • Kyu-Won Kim,

    Affiliation: Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea

    X
  • Sungwon Kim,

    Affiliation: Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • David Langenberger,

    Affiliation: Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    X
  • Mi-Kyung Lee,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Taeheon Lee,

    Affiliation: Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea

    X
  • Shrinivasrao Mane,

    Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Guillaume Marcais,

    Affiliation: Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America

    X
  • Manja Marz,

    Affiliations: Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany, Philipps-Universität Marburg, Pharmazeutische Chemie, Marburg, Germany

    X
  • Audrey P. McElroy,

    Affiliation: Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Thero Modise,

    Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Mikhail Nefedov,

    Affiliation: Children's Hospital and Research Center at Oakland, Oakland, California, United States of America

    X
  • Cédric Notredame,

    Affiliation: Comparative Bioinformatics, Centre for Genomic Regulation (CRG), Universitat Pompeus Fabre, Barcelona, Spain

    X
  • Ian R. Paton,

    Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom

    X
  • William S. Payne,

    Affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America

    X
  • Geo Pertea,

    Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

    X
  • Dennis Prickett,

    Affiliation: Institute for Animal Health, Compton, Berkshire, United Kingdom

    X
  • Daniela Puiu,

    Affiliation: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America

    X
  • Dan Qioa,

    Affiliation: Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Emanuele Raineri,

    Affiliation: Comparative Bioinformatics, Centre for Genomic Regulation (CRG), Universitat Pompeus Fabre, Barcelona, Spain

    X
  • Magali Ruffier,

    Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Steven L. Salzberg,

    Affiliation: Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, United States of America

    X
  • Michael C. Schatz,

    Affiliation: Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, United States of America

    X
  • Chantel Scheuring,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Carl J. Schmidt,

    Affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America

    X
  • Steven Schroeder,

    Affiliation: Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America

    X
  • Stephen M. J. Searle,

    Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Edward J. Smith,

    Affiliation: Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Jacqueline Smith,

    Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom

    X
  • Tad S. Sonstegard,

    Affiliation: Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America

    X
  • Peter F. Stadler,

    Affiliations: Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany, Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany, Department of Theoretical Chemistry University of Vienna, Vienna, Austria, Santa Fe Institute, Santa Fe, New Mexico, United States of America

    X
  • Hakim Tafer,

    Affiliations: Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany, Department of Theoretical Chemistry University of Vienna, Vienna, Austria

    X
  • Zhijian (Jake) Tu,

    Affiliation: Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Curtis P. Van Tassell,

    Affiliations: Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America, Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America

    X
  • Albert J. Vilella,

    Affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

    X
  • Kelly P. Williams,

    Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • James A. Yorke,

    Affiliation: Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America

    X
  • Liqing Zhang,

    Affiliation: Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America

    X
  • Hong-Bin Zhang,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Xiaojun Zhang,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Yang Zhang,

    Affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America

    X
  • Kent M. Reed mail

    reedx054@umn.edu

    Affiliation: Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America

    X
  • Published: September 07, 2010
  • DOI: 10.1371/journal.pbio.1000475

About the Authors

Rami A. Dalloul, Sungwon Kim, Audrey P. McElroy, Edward J. Smith
Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
Julie A. Long, Le Ann Blomberg
Animal Biosciences and Biotechnology Laboratory, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
Aleksey V. Zimin, Guillaume Marcais, James A. Yorke
Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
Luqman Aslam, Richard P. M. A. Crooijmans, Martien A. M. Groenen, Hendrik-Jan Megens
Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
Kathryn Beal, Paul Flicek, Javier Herrero, Albert J. Vilella
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Pascal Bouffard, Karin M. Frederickson, Tim T. Harkins
Roche Applied Science, Indianapolis, Indiana, United States of America
David W. Burt, Ian R. Paton, Jacqueline Smith
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom
Oswald Crasta, Kristal Cooper, Clive Evans, Otto Folkerts, Shrinivasrao Mane, Thero Modise, Kelly P. Williams
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America
Oswald Crasta, Otto Folkerts
Chromatin Inc., Champaign, Illinois, United States of America
Roger A. Coulombe
Department of Veterinary Sciences, Utah State University, Logan, Utah, United States of America
Supriyo De
Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
Mary E. Delany, Andrew Jiang
Department of Animal Science, University of California, Davis, California, United States of America
Jerry B. Dodgson, William S. Payne
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
Jennifer J. Dong, Mi-Kyung Lee, Chantel Scheuring, Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang
Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
Liliana Florea, Geo Pertea, Daniela Puiu
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
Steve Hoffmann, David Langenberger, Manja Marz, Peter F. Stadler, Hakim Tafer
Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
Steve Hoffmann
LIFE Project, University of Leipzig, Leipzig, Germany
Pieter de Jong, Mikhail Nefedov
Children's Hospital and Research Center at Oakland, Oakland, California, United States of America
Pete Kaiser, Dennis Prickett
Institute for Animal Health, Compton, Berkshire, United Kingdom
Heebal Kim, Kyu-Won Kim, Taeheon Lee
Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
Manja Marz
Philipps-Universität Marburg, Pharmazeutische Chemie, Marburg, Germany
Cédric Notredame, Emanuele Raineri
Comparative Bioinformatics, Centre for Genomic Regulation (CRG), Universitat Pompeus Fabre, Barcelona, Spain
Dan Qioa, Liqing Zhang
Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
Magali Ruffier, Stephen M. J. Searle
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Steven L. Salzberg, Michael C. Schatz
Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
Carl J. Schmidt
Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, United States of America
Steven Schroeder, Tad S. Sonstegard, Curtis P. Van Tassell
Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America
Peter F. Stadler
Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
Peter F. Stadler
Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
Peter F. Stadler, Hakim Tafer
Department of Theoretical Chemistry University of Vienna, Vienna, Austria
Peter F. Stadler
Santa Fe Institute, Santa Fe, New Mexico, United States of America
Zhijian (Jake) Tu
Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
Curtis P. Van Tassell
Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland, United States of America
Kent M. Reed
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America

Corresponding Author

Email: reedx054@umn.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

The author(s) have made the following declarations about their contributions: Conceived and designed the experiments: RD AVZ DWB RAC MD JD OF MG SLS SS EJS CPVT HBZ KMR. Performed the experiments: LAB OC RC KC SD JJD CE TTH AJ SPM WSP CS SGS TS XZ YZ. Analyzed the data: AVZ LA KB RC RAC PF LF JH SH HJM PK HK KWK SK DL MKL TL GM MM APM TM CN IRP GP DP DP DQ ER MR MCS CS SS JS PFS HT ZT AJV KPW JAY LZ. Contributed reagents/materials/analysis tools: PJdJ MN KMR. Wrote the paper: RD JAL AVZ DWB JD HT JH SS CS ZT KPW LZ MG KMR.