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Research Article

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

  • Rays H. Y. Jiang equal contributor,

    equal contributor Contributed equally to this work with: Rays H. Y. Jiang, Irene de Bruijn, Brian J. Haas

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

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  • Irene de Bruijn equal contributor,

    equal contributor Contributed equally to this work with: Rays H. Y. Jiang, Irene de Bruijn, Brian J. Haas

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

    Current address: Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.

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  • Brian J. Haas equal contributor,

    equal contributor Contributed equally to this work with: Rays H. Y. Jiang, Irene de Bruijn, Brian J. Haas

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

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  • Rodrigo Belmonte,

    Affiliations: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom, Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Lars Löbach,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • James Christie,

    Affiliations: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom, Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Guido van den Ackerveken,

    Affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands

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  • Arnaud Bottin,

    Affiliation: Université de Toulouse; UPS; Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France and CNRS, Laboratoire de Recherche en Sciences Végétales, Auzeville, Castanet-Tolosan, France

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  • Vincent Bulone,

    Affiliation: Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden

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  • Sara M. Díaz-Moreno,

    Affiliation: Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden

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  • Bernard Dumas,

    Affiliation: Université de Toulouse; UPS; Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France and CNRS, Laboratoire de Recherche en Sciences Végétales, Auzeville, Castanet-Tolosan, France

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  • Lin Fan,

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

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  • Elodie Gaulin,

    Affiliation: Université de Toulouse; UPS; Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France and CNRS, Laboratoire de Recherche en Sciences Végétales, Auzeville, Castanet-Tolosan, France

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  • Francine Govers,

    Affiliations: Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands, Centre for BioSystems Genomics, Wageningen, The Netherlands

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  • Laura J. Grenville-Briggs,

    Affiliations: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom, Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden

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  • Neil R. Horner,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Joshua Z. Levin,

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

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  • Marco Mammella,

    Affiliation: Dipartimento di Gestione dei Sistemi Agrari e Forestali, Università degli Studi Mediterranea, Reggio Calabria, Italy

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  • Harold J. G. Meijer,

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

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  • Paul Morris,

    Affiliation: Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America

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  • Chad Nusbaum,

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

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  • Stan Oome,

    Affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands

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  • Andrew J. Phillips,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • David van Rooyen,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Elzbieta Rzeszutek,

    Affiliation: Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden

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  • Marcia Saraiva,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Chris J. Secombes,

    Affiliation: Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Michael F. Seidl,

    Affiliations: Centre for BioSystems Genomics, Wageningen, The Netherlands, Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands

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  • Berend Snel,

    Affiliations: Centre for BioSystems Genomics, Wageningen, The Netherlands, Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands

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  • Joost H. M. Stassen,

    Affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands

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  • Sean Sykes,

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

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  • Sucheta Tripathy,

    Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America

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  • Herbert van den Berg,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Julio C. Vega-Arreguin,

    Affiliation: ENES Unidad León, Universidad Nacional Autónoma de México, León, Mexico

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  • Stephan Wawra,

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

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  • Sarah K. Young,

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

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  • Qiandong Zeng,

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

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  • Javier Dieguez-Uribeondo,

    Affiliation: Departamento de Micología, Real Jardín Botánico CSIC, Madrid, Spain

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  • Carsten Russ ,

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

    * These authors also contributed equally to this work.

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  • Brett M. Tyler ,

    Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America

    Current address: Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.

    * These authors also contributed equally to this work.

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  • Pieter van West mail

    p.vanwest@abdn.ac.uk

    Affiliation: Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom

    * These authors also contributed equally to this work.

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  • Published: June 13, 2013
  • DOI: 10.1371/journal.pgen.1003272

About the Authors

Rays H. Y. Jiang, Brian J. Haas, Lin Fan, Joshua Z. Levin, Chad Nusbaum, Sean Sykes, Sarah K. Young, Qiandong Zeng, Carsten Russ
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
Irene de Bruijn, Rodrigo Belmonte, Lars Löbach, James Christie, Laura J. Grenville-Briggs, Neil R. Horner, Andrew J. Phillips, David van Rooyen, Marcia Saraiva, Herbert van den Berg, Stephan Wawra, Pieter van West
Aberdeen Oomycete Laboratory, School of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
Rodrigo Belmonte, James Christie, Chris J. Secombes
Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
Guido van den Ackerveken, Stan Oome, Joost H. M. Stassen
Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
Arnaud Bottin, Bernard Dumas, Elodie Gaulin
Université de Toulouse; UPS; Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France and CNRS, Laboratoire de Recherche en Sciences Végétales, Auzeville, Castanet-Tolosan, France
Vincent Bulone, Sara M. Díaz-Moreno, Laura J. Grenville-Briggs, Elzbieta Rzeszutek
Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
Francine Govers, Harold J. G. Meijer
Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
Francine Govers, Michael F. Seidl, Berend Snel
Centre for BioSystems Genomics, Wageningen, The Netherlands
Marco Mammella
Dipartimento di Gestione dei Sistemi Agrari e Forestali, Università degli Studi Mediterranea, Reggio Calabria, Italy
Paul Morris
Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
Michael F. Seidl, Berend Snel
Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands
Sucheta Tripathy, Brett M. Tyler
Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
Julio C. Vega-Arreguin
ENES Unidad León, Universidad Nacional Autónoma de México, León, Mexico
Javier Dieguez-Uribeondo
Departamento de Micología, Real Jardín Botánico CSIC, Madrid, Spain

Corresponding Author

Email: p.vanwest@abdn.ac.uk

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: RHYJ IdB BJH CJS JD-U CR BMT PvW VB ER SMD-M. Performed the experiments: RHYJ IdB BJH RB LL JC JZL CJS SW SKY QZ CR BMT PvW ER SMD-M AJP. Analyzed the data: RHYJ IdB BJH RB LL JC GvdA AB BD LF EG FG LJG-B NRH JZL MM HJGM PM CN SO DvR MS CJS MFS BS JHMS SS ST HvdB JCV-A SW SKY QZ JD-U CR BMT PvW VB ER SMD-M. Contributed reagents/materials/analysis tools: CN CR BMT PvW ER SMD-M AJP. Wrote the paper: RHYJ IdB BJH RB LL FG CN CR BMT PvW VB.