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Research Article

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

  • Joyce E. Loper mail,

    Joyce.Loper@ars.usda.gov

    Affiliations: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

    X
  • Karl A. Hassan,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Dmitri V. Mavrodi,

    Affiliation: Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America

    X
  • Edward W. Davis II,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America

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  • Chee Kent Lim,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

    X
  • Brenda T. Shaffer,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America

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  • Liam D. H. Elbourne,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Virginia O. Stockwell,

    Affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

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  • Sierra L. Hartney,

    Affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

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  • Katy Breakwell,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Marcella D. Henkels,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America

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  • Sasha G. Tetu,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Lorena I. Rangel,

    Affiliation: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

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  • Teresa A. Kidarsa,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America

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  • Neil L. Wilson,

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Judith E. van de Mortel,

    Affiliation: Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

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  • Chunxu Song,

    Affiliation: Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

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  • Rachel Blumhagen,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America

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  • Diana Radune,

    Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America

    X
  • Jessica B. Hostetler,

    Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Lauren M. Brinkac,

    Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • A. Scott Durkin,

    Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America

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  • Daniel A. Kluepfel,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Davis, California, United States of America

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  • W. Patrick Wechter,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Charleston, South Carolina, United States of America

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  • Anne J. Anderson,

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

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  • Young Cheol Kim,

    Affiliation: Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju, Korea

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  • Leland S. Pierson III,

    Affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America

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  • Elizabeth A. Pierson,

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

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  • Steven E. Lindow,

    Affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America

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  • Donald Y. Kobayashi,

    Affiliation: Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America

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  • Jos M. Raaijmakers,

    Affiliation: Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

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  • David M. Weller,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America

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  • Linda S. Thomashow,

    Affiliation: Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America

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  • Andrew E. Allen,

    Affiliation: The J. Craig Venter Institute, San Diego, California, United States of America

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  • Ian T. Paulsen

    Affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia

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  • Published: July 05, 2012
  • DOI: 10.1371/journal.pgen.1002784

About the Authors

Joyce E. Loper, Edward W. Davis II, Brenda T. Shaffer, Marcella D. Henkels, Teresa A. Kidarsa, Rachel Blumhagen
Agricultural Research Service, U.S. Department of Agriculture, Corvallis, Oregon, United States of America
Joyce E. Loper, Virginia O. Stockwell, Sierra L. Hartney, Lorena I. Rangel
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
Karl A. Hassan, Chee Kent Lim, Liam D. H. Elbourne, Katy Breakwell, Sasha G. Tetu, Neil L. Wilson, Ian T. Paulsen
Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
Dmitri V. Mavrodi
Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
Judith E. van de Mortel, Chunxu Song, Jos M. Raaijmakers
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
Diana Radune, Jessica B. Hostetler, Lauren M. Brinkac, A. Scott Durkin
The J. Craig Venter Institute, Rockville, Maryland, United States of America
Daniel A. Kluepfel
Agricultural Research Service, U.S. Department of Agriculture, Davis, California, United States of America
W. Patrick Wechter
Agricultural Research Service, U.S. Department of Agriculture, Charleston, South Carolina, United States of America
Anne J. Anderson
Department of Biology, Utah State University, Logan, Utah, United States of America
Young Cheol Kim
Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju, Korea
Leland S. Pierson III
Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
Elizabeth A. Pierson
Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
Steven E. Lindow
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
Donald Y. Kobayashi
Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
David M. Weller, Linda S. Thomashow
Agricultural Research Service, U.S. Department of Agriculture, Pullman, Washington, United States of America
Andrew E. Allen
The J. Craig Venter Institute, San Diego, California, United States of America

Corresponding Author

Email: Joyce.Loper@ars.usda.gov

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: JEL KAH DVM EWD BTS VOS MDH TAK EAP LSP JMR LST AEA ITP DYK. Performed the experiments: KAH DVM EWD BTS VOS MDH TAK KB LIR JEvdM RB. Analyzed the data: JEL KAH DVM EWD CKL LDHE SLH SGT NLW DR JBH LMB ASD CKL BTS VOS MDH CS JEvdM JMR. Contributed reagents/materials/analysis tools: DAK WPW AJA YCK LSP SEL DMW DYK. Wrote the paper: JEL KAH DVM EWD LST ITP.