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Research Article

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

  • Estienne C. Swart,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • John R. Bracht,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Vincent Magrini,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Patrick Minx,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Xiao Chen,

    Affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Yi Zhou,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Jaspreet S. Khurana,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Aaron D. Goldman,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Mariusz Nowacki,

    Affiliations: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America, Institute of Cell Biology, University of Bern, Bern, Switzerland

    X
  • Klaas Schotanus,

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Seolkyoung Jung,

    Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America

    X
  • Robert S. Fulton,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Amy Ly,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Sean McGrath,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Kevin Haub,

    Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Jessica L. Wiggins,

    Affiliation: Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

    X
  • Donna Storton,

    Affiliation: Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

    X
  • John C. Matese,

    Affiliation: Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

    X
  • Lance Parsons,

    Affiliation: Bioinformatics Group, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America

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  • Wei-Jen Chang,

    Affiliation: Department of Biology, Hamilton College, Clinton, New York, United States of America

    X
  • Michael S. Bowen,

    Affiliation: Biology Department, Bradley University, Peoria, Illinois, United States of America

    X
  • Nicholas A. Stover,

    Affiliation: Biology Department, Bradley University, Peoria, Illinois, United States of America

    X
  • Thomas A. Jones,

    Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America

    X
  • Sean R. Eddy,

    Affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America

    X
  • Glenn A. Herrick,

    Affiliation: Biology Department, University of Utah, Salt Lake City, Utah, United States of America

    X
  • Thomas G. Doak,

    Affiliation: Department of Biology, University of Indiana, Bloomington, Indiana, United States of America

    X
  • Richard K. Wilson,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

    X
  • Elaine R. Mardis,

    Affiliations: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America

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  • Laura F. Landweber mail

    lfl@princeton.edu

    Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America

    X
  • Published: January 29, 2013
  • DOI: 10.1371/journal.pbio.1001473

About the Authors

Estienne C. Swart, John R. Bracht, Yi Zhou, Jaspreet S. Khurana, Aaron D. Goldman, Mariusz Nowacki, Klaas Schotanus, Laura F. Landweber
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
Vincent Magrini, Patrick Minx, Robert S. Fulton, Amy Ly, Sean McGrath, Kevin Haub, Richard K. Wilson, Elaine R. Mardis
The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
Vincent Magrini, Robert S. Fulton, Richard K. Wilson, Elaine R. Mardis
Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
Xiao Chen
Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
Mariusz Nowacki
Institute of Cell Biology, University of Bern, Bern, Switzerland
Seolkyoung Jung, Thomas A. Jones, Sean R. Eddy
Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
Jessica L. Wiggins, Donna Storton, John C. Matese
Sequencing Core Facility, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
Lance Parsons
Bioinformatics Group, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
Wei-Jen Chang
Department of Biology, Hamilton College, Clinton, New York, United States of America
Michael S. Bowen, Nicholas A. Stover
Biology Department, Bradley University, Peoria, Illinois, United States of America
Glenn A. Herrick
Biology Department, University of Utah, Salt Lake City, Utah, United States of America
Thomas G. Doak
Department of Biology, University of Indiana, Bloomington, Indiana, United States of America

Corresponding Author

Email: lfl@princeton.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: Designed the software used in analysis: ECS. Conceived and designed the experiments: ECS VM YZ TGD JRB RKW ERM LFL. Performed the experiments: ECS JRB VM TGD JSK MN KS AL SM KH JLB DS. Analyzed the data: ECS VM PM XC YZ ADG SJ WC RSF. Contributed reagents/materials/analysis tools: ECS JRB MN KS VM AL SM KH JCM LP TGD SJ TAJ SRE MSB NAS. Wrote the paper: ECS JRB VM XC TGD GAH LFL.