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Research Article

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

  • Li-Jun Ma mail,

    lijun@broad.mit.edu (LJM); wickes@uthscsa.edu (BLW)

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

    X
  • Ashraf S. Ibrahim,

    Affiliation: Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, United States of America

    X
  • Christopher Skory,

    Affiliation: Bioproducts and Biocatalysis Research, National Center for Agricultural Utilization Research, USDA-ARS, Midwest Area, Peoria, Illinois, United States of America

    X
  • Manfred G. Grabherr,

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

    X
  • Gertraud Burger,

    Affiliation: Department of Biochemistry, Université de Montréal, Montreal, Canada

    X
  • Margi Butler,

    Affiliation: Department of Biochemistry, University of Otago, Otago, New Zealand

    X
  • Marek Elias,

    Affiliation: Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic

    X
  • Alexander Idnurm,

    Affiliation: Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri, United States of America

    X
  • B. Franz Lang,

    Affiliation: Department of Biochemistry, Université de Montréal, Montreal, Canada

    X
  • Teruo Sone,

    Affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan

    X
  • Ayumi Abe,

    Affiliation: Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan

    X
  • Sarah E. Calvo,

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

    X
  • Luis M. Corrochano,

    Affiliation: Departamento de Genética, Universidad de Sevilla, Sevilla, Spain

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  • Reinhard Engels,

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

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  • Jianmin Fu,

    Affiliation: Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America

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  • Wilhelm Hansberg,

    Affiliation: Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico

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  • Jung-Mi Kim,

    Affiliation: Department of Plant Biology, University of California Davis, Davis, California, United States of America

    X
  • Chinnappa D. Kodira,

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

    X
  • Michael J. Koehrsen,

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

    X
  • Bo Liu,

    Affiliation: Department of Plant Biology, University of California Davis, Davis, California, United States of America

    X
  • Diego Miranda-Saavedra,

    Affiliation: Cambridge Institute for Medical Research, Cambridge, United Kingdom

    X
  • Sinead O'Leary,

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

    X
  • Lucila Ortiz-Castellanos,

    Affiliation: Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico

    X
  • Russell Poulter,

    Affiliation: Department of Biochemistry, University of Otago, Otago, New Zealand

    X
  • Julio Rodriguez-Romero,

    Affiliation: Departamento de Genética, Universidad de Sevilla, Sevilla, Spain

    X
  • José Ruiz-Herrera,

    Affiliation: Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico

    X
  • Yao-Qing Shen,

    Affiliation: Department of Biochemistry, Université de Montréal, Montreal, Canada

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  • Qiandong Zeng,

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

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  • James Galagan,

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

    X
  • Bruce W. Birren,

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

    X
  • Christina A. Cuomo equal contributor,

    equal contributor Contributed equally to this work with: Christina A. Cuomo, Brian L. Wickes

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

    X
  • Brian L. Wickes equal contributor mail

    equal contributor Contributed equally to this work with: Christina A. Cuomo, Brian L. Wickes

    lijun@broad.mit.edu (LJM); wickes@uthscsa.edu (BLW)

    Affiliation: Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America

    X
  • Published: July 03, 2009
  • DOI: 10.1371/journal.pgen.1000549

About the Authors

Li-Jun Ma, Manfred G. Grabherr, Sarah E. Calvo, Reinhard Engels, Chinnappa D. Kodira, Michael J. Koehrsen, Sinead O'Leary, Qiandong Zeng, James Galagan, Bruce W. Birren, Christina A. Cuomo
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Ashraf S. Ibrahim
Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, California, United States of America
Christopher Skory
Bioproducts and Biocatalysis Research, National Center for Agricultural Utilization Research, USDA-ARS, Midwest Area, Peoria, Illinois, United States of America
Gertraud Burger, B. Franz Lang, Yao-Qing Shen
Department of Biochemistry, Université de Montréal, Montreal, Canada
Margi Butler, Russell Poulter
Department of Biochemistry, University of Otago, Otago, New Zealand
Marek Elias
Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
Alexander Idnurm
Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri, United States of America
Teruo Sone, Ayumi Abe
Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
Luis M. Corrochano, Julio Rodriguez-Romero
Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
Jianmin Fu, Brian L. Wickes
Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
Wilhelm Hansberg
Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
Jung-Mi Kim, Bo Liu
Department of Plant Biology, University of California Davis, Davis, California, United States of America
Diego Miranda-Saavedra
Cambridge Institute for Medical Research, Cambridge, United Kingdom
Lucila Ortiz-Castellanos, José Ruiz-Herrera
Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: LJM CS BWB BLW. Performed the experiments: LJM BFL TS AA JF. Analyzed the data: LJM ASI MGG GB MB ME AI TS SEC LMC WH JMK BL DMS LOC RP JRR JRH YQS CAC. Contributed reagents/materials/analysis tools: ASI CS MGG BFL RE CDK MJK SO QZ JG BLW. Wrote the paper: LJM ASI CS ME AI BL CAC BLW.