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Research Article

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

  • Jeffrey J. Coleman equal contributor,

    equal contributor Contributed equally to this work with: Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres

    Affiliations: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America, Massachusetts General Hospital, Boston, Massachusetts, United States of America

    X
  • Steve D. Rounsley equal contributor,

    equal contributor Contributed equally to this work with: Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres

    Affiliation: BIO5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Marianela Rodriguez-Carres equal contributor,

    equal contributor Contributed equally to this work with: Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres

    Affiliations: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America, Department of Biology, Duke University, Durham, North Carolina, United States of America

    X
  • Alan Kuo,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • Catherine C. Wasmann,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Jane Grimwood,

    Affiliations: Joint Genome Institute—Stanford Human Genome Center, Palo Alto, California, United States of America, Hudson Alpha Genome Sequencing Center, Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America

    X
  • Jeremy Schmutz,

    Affiliations: Joint Genome Institute—Stanford Human Genome Center, Palo Alto, California, United States of America, Hudson Alpha Genome Sequencing Center, Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America

    X
  • Masatoki Taga,

    Affiliation: Department of Biology, Okayama University, Okayama, Japan

    X
  • Gerard J. White,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Shiguo Zhou,

    Affiliation: Laboratory for Molecule and Computational Genomics, University of Wisconsin, Madison, Wisconsin, United States of America

    X
  • David C. Schwartz,

    Affiliation: Laboratory for Molecule and Computational Genomics, University of Wisconsin, Madison, Wisconsin, United States of America

    X
  • Michael Freitag,

    Affiliation: Department of Biochemistry and Biophysics and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America

    X
  • Li-jun Ma,

    Affiliation: The Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Etienne G. J. Danchin,

    Affiliations: Architecture et Fonction des Macromolécules Biologiques, CNRS, Universités Aix-Marseille I & II, Marseille, France, Institut National de la Recherche Agronomique, Centre de recherche de Sophia-Antipolis, Sophia-Antipolis, France

    X
  • Bernard Henrissat,

    Affiliation: Architecture et Fonction des Macromolécules Biologiques, CNRS, Universités Aix-Marseille I & II, Marseille, France

    X
  • Pedro M. Coutinho,

    Affiliation: Architecture et Fonction des Macromolécules Biologiques, CNRS, Universités Aix-Marseille I & II, Marseille, France

    X
  • David R. Nelson,

    Affiliation: Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee, United States of America

    X
  • Dave Straney,

    Affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America

    X
  • Carolyn A. Napoli,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Bridget M. Barker,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Michael Gribskov,

    Affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America

    X
  • Martijn Rep,

    Affiliation: Plant Pathology, University of Amsterdam, Amsterdam, The Netherlands

    X
  • Scott Kroken,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • István Molnár,

    Affiliation: South West Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, University of Arizona, Tucson, Arizona, United States of America

    X
  • Christopher Rensing,

    Affiliation: Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, United States of America

    X
  • John C. Kennell,

    Affiliation: Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America

    X
  • Jorge Zamora,

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Mark L. Farman,

    Affiliation: Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America

    X
  • Eric U. Selker,

    Affiliation: Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America

    X
  • Asaf Salamov,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • Harris Shapiro,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • Jasmyn Pangilinan,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • Erika Lindquist,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • Casey Lamers,

    Affiliation: Laboratory for Molecule and Computational Genomics, University of Wisconsin, Madison, Wisconsin, United States of America

    X
  • Igor V. Grigoriev,

    Affiliation: United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America

    X
  • David M. Geiser,

    Affiliation: Fusarium Research Center, Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania, United States of America

    X
  • Sarah F. Covert,

    Affiliation: Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America

    X
  • Esteban Temporini,

    Affiliations: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America, Vilmorin Inc., Tucson, Arizona, United States of America

    X
  • Hans D. VanEtten mail

    vanetten@ag.arizona.edu

    Affiliation: Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America

    X
  • Published: August 28, 2009
  • DOI: 10.1371/journal.pgen.1000618

About the Authors

Jeffrey J. Coleman, Marianela Rodriguez-Carres, Catherine C. Wasmann, Gerard J. White, Carolyn A. Napoli, Bridget M. Barker, Scott Kroken, Jorge Zamora, Esteban Temporini, Hans D. VanEtten
Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
Jeffrey J. Coleman
Massachusetts General Hospital, Boston, Massachusetts, United States of America
Steve D. Rounsley
BIO5 Institute and Department of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
Marianela Rodriguez-Carres
Department of Biology, Duke University, Durham, North Carolina, United States of America
Alan Kuo, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Igor V. Grigoriev
United States Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
Jane Grimwood, Jeremy Schmutz
Joint Genome Institute—Stanford Human Genome Center, Palo Alto, California, United States of America
Jane Grimwood, Jeremy Schmutz
Hudson Alpha Genome Sequencing Center, Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
Masatoki Taga
Department of Biology, Okayama University, Okayama, Japan
Shiguo Zhou, David C. Schwartz, Casey Lamers
Laboratory for Molecule and Computational Genomics, University of Wisconsin, Madison, Wisconsin, United States of America
Michael Freitag
Department of Biochemistry and Biophysics and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
Li-jun Ma
The Broad Institute, Cambridge, Massachusetts, United States of America
Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho
Architecture et Fonction des Macromolécules Biologiques, CNRS, Universités Aix-Marseille I & II, Marseille, France
Etienne G. J. Danchin
Institut National de la Recherche Agronomique, Centre de recherche de Sophia-Antipolis, Sophia-Antipolis, France
David R. Nelson
Department of Molecular Sciences, University of Tennessee, Memphis, Tennessee, United States of America
Dave Straney
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
Michael Gribskov
Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
Martijn Rep
Plant Pathology, University of Amsterdam, Amsterdam, The Netherlands
István Molnár
South West Center for Natural Products Research and Commercialization, Office of Arid Lands Studies, University of Arizona, Tucson, Arizona, United States of America
Christopher Rensing
Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, United States of America
John C. Kennell
Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
Mark L. Farman
Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
Eric U. Selker
Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
David M. Geiser
Fusarium Research Center, Department of Plant Pathology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
Sarah F. Covert
Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
Esteban Temporini
Vilmorin Inc., Tucson, Arizona, United States of America

Corresponding Author

Email: vanetten@ag.arizona.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: CCW DMG SFC ET HDV. Performed the experiments: JJC SDR MRC JS MT GJW SZ MF LjM EGJD DRN DS BMB MR JZ MLF AS HS JP EL CL. Analyzed the data: JJC SDR MRC AK CCW JG MT GJW SZ DCS MF LjM EGJD BH PMC DRN DS CAN BMB MG MR SK IM CR JCK JZ MLF EUS EL IVG SFC. Contributed reagents/materials/analysis tools: PMC. Wrote the paper: JJC MRC CCW GJW HDV.