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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Author

Listed:
  • Brian J. Haas

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Sophien Kamoun

    (The Sainsbury Laboratory
    The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • Michael C. Zody

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Uppsala University, Box 597, Uppsala SE-751 24, Sweden)

  • Rays H. Y. Jiang

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Laboratory of Phytopathology, Wageningen University, 1-6708 PB, Wageningen, The Netherlands)

  • Robert E. Handsaker

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Liliana M. Cano

    (The Sainsbury Laboratory)

  • Manfred Grabherr

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Chinnappa D. Kodira

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Present addresses: 454 Life Sciences, Branford, Connecticut 06405, USA (C.D.K.); Virginia Bioinformatics Institute, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, USA (T.T.-A.); Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland (K.O.).)

  • Sylvain Raffaele

    (The Sainsbury Laboratory)

  • Trudy Torto-Alalibo

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA
    Present addresses: 454 Life Sciences, Branford, Connecticut 06405, USA (C.D.K.); Virginia Bioinformatics Institute, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, USA (T.T.-A.); Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland (K.O.).)

  • Tolga O. Bozkurt

    (The Sainsbury Laboratory)

  • Audrey M. V. Ah-Fong

    (University of California, Riverside, California 92521, USA)

  • Lucia Alvarado

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Vicky L. Anderson

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Miles R. Armstrong

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Anna Avrova

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Laura Baxter

    (University of Warwick, Wellesbourne, Warwick CV35 9EF, UK)

  • Jim Beynon

    (University of Warwick, Wellesbourne, Warwick CV35 9EF, UK)

  • Petra C. Boevink

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Stephanie R. Bollmann

    (Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA)

  • Jorunn I. B. Bos

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • Vincent Bulone

    (Royal Institute of Technology (KTH), School of Biotechnology, AlbaNova University Centre)

  • Guohong Cai

    (Cornell University, Ithaca, New York 14853, USA)

  • Cahid Cakir

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • James C. Carrington

    (Oregon State University, Corvallis, Oregon 97331, USA)

  • Megan Chawner

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Lucio Conti

    (Plant Molecular Sciences Faculty of Biomedical and Life Sciences, Bower Building, University of Glasgow)

  • Stefano Costanzo

    (USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160, USA)

  • Richard Ewan

    (Plant Molecular Sciences Faculty of Biomedical and Life Sciences, Bower Building, University of Glasgow)

  • Noah Fahlgren

    (Oregon State University, Corvallis, Oregon 97331, USA)

  • Michael A. Fischbach

    (Massachusetts General Hospital, Boston, Massachsetts 02114, USA)

  • Johanna Fugelstad

    (Royal Institute of Technology (KTH), School of Biotechnology, AlbaNova University Centre)

  • Eleanor M. Gilroy

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Sante Gnerre

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Pamela J. Green

    (Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA)

  • Laura J. Grenville-Briggs

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • John Griffith

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Niklaus J. Grünwald

    (Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA)

  • Karolyn Horn

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Neil R. Horner

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Chia-Hui Hu

    (North Carolina State University, Raleigh, North Carolina 27695, USA)

  • Edgar Huitema

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • Dong-Hoon Jeong

    (Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA)

  • Alexandra M. E. Jones

    (The Sainsbury Laboratory)

  • Jonathan D. G. Jones

    (The Sainsbury Laboratory)

  • Richard W. Jones

    (USDA-ARS, Beltsville, Maryland 20705, USA)

  • Elinor K. Karlsson

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Sridhara G. Kunjeti

    (University of Delaware, Newark, Delaware 19716, USA)

  • Kurt Lamour

    (University of Tennessee, Knoxville, Tennessee 37996, USA)

  • Zhenyu Liu

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • LiJun Ma

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Daniel MacLean

    (The Sainsbury Laboratory)

  • Marcus C. Chibucos

    (Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA)

  • Hayes McDonald

    (Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA)

  • Jessica McWalters

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Harold J. G. Meijer

    (Laboratory of Phytopathology, Wageningen University, 1-6708 PB, Wageningen, The Netherlands)

  • William Morgan

    (The College of Wooster, Wooster, Ohio 44691, USA)

  • Paul F. Morris

    (Bowling Green State University, Bowling Green, Ohio 43403, USA)

  • Carol A. Munro

    (University of Aberdeen, School of Medical Sciences, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Keith O’Neill

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Present addresses: 454 Life Sciences, Branford, Connecticut 06405, USA (C.D.K.); Virginia Bioinformatics Institute, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, USA (T.T.-A.); Biomedical Diagnostics Institute, Dublin City University, Dublin 9, Ireland (K.O.).)

  • Manuel Ospina-Giraldo

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Andrés Pinzón

    (Mycology and Phytopathology Laboratory, Los Andes University)

  • Leighton Pritchard

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Bernard Ramsahoye

    (Institute of Genetics and Molecular Medicine, University of Edinburgh, Cancer Research Centre, Western General Hospital)

  • Qinghu Ren

    (J. Craig Venter Institute, Rockville, Maryland 20850, USA)

  • Silvia Restrepo

    (Mycology and Phytopathology Laboratory, Los Andes University)

  • Sourav Roy

    (University of California, Riverside, California 92521, USA)

  • Ari Sadanandom

    (Plant Molecular Sciences Faculty of Biomedical and Life Sciences, Bower Building, University of Glasgow)

  • Alon Savidor

    (Tel Aviv University)

  • Sebastian Schornack

    (The Sainsbury Laboratory)

  • David C. Schwartz

    (Laboratory of Genetics, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin-Madison)

  • Ulrike D. Schumann

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Ben Schwessinger

    (The Sainsbury Laboratory)

  • Lauren Seyer

    (Lafayette College, Easton, Pennsylvania 18042, USA)

  • Ted Sharpe

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Cristina Silvar

    (The Sainsbury Laboratory)

  • Jing Song

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • David J. Studholme

    (The Sainsbury Laboratory)

  • Sean Sykes

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

  • Marco Thines

    (The Sainsbury Laboratory
    University of Hohenheim, Institute of Botany 210)

  • Peter J. I. van de Vondervoort

    (Laboratory of Phytopathology, Wageningen University, 1-6708 PB, Wageningen, The Netherlands)

  • Vipaporn Phuntumart

    (Bowling Green State University, Bowling Green, Ohio 43403, USA)

  • Stephan Wawra

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Rob Weide

    (Laboratory of Phytopathology, Wageningen University, 1-6708 PB, Wageningen, The Netherlands)

  • Joe Win

    (The Sainsbury Laboratory)

  • Carolyn Young

    (The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA)

  • Shiguo Zhou

    (Laboratory of Genetics, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin-Madison)

  • William Fry

    (Cornell University, Ithaca, New York 14853, USA)

  • Blake C. Meyers

    (Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA)

  • Pieter van West

    (University of Aberdeen, Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK)

  • Jean Ristaino

    (North Carolina State University, Raleigh, North Carolina 27695, USA)

  • Francine Govers

    (Laboratory of Phytopathology, Wageningen University, 1-6708 PB, Wageningen, The Netherlands)

  • Paul R. J. Birch

    (College of Life Sciences, University of Dundee (at SCRI), Invergowrie, Dundee DD2 5DA, UK)

  • Stephen C. Whisson

    (Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK)

  • Howard S. Judelson

    (University of California, Riverside, California 92521, USA)

  • Chad Nusbaum

    (Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA)

Abstract

Blighted harvest: genome sequence unearths roots of potato pathogen's adaptability The genome of Phytophthora infestans, the pathogen that triggered the Irish potato famine in the nineteenth century, has been sequenced. It remains a devastating pathogen, with late blight destroying crops worth billions of dollars each year. Blight is difficult to control, in part because it adapts so quickly to genetically resistant potato strains. Comparison with two other Phytophthora genomes shows rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes induced during infection that have activities thought to alter host physiology. These fast evolving effector genes are found in highly dynamic and expanded regions of the genome, a factor that may contribute to its rapid adaptability to host plants. The P. infestans genome is the biggest so far sequenced, at about 240 megabases, with an extremely high repeat content of close to 75%. It is a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes related to organisms such as brown algae and diatoms.

Suggested Citation

  • Brian J. Haas & Sophien Kamoun & Michael C. Zody & Rays H. Y. Jiang & Robert E. Handsaker & Liliana M. Cano & Manfred Grabherr & Chinnappa D. Kodira & Sylvain Raffaele & Trudy Torto-Alalibo & Tolga O., 2009. "Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans," Nature, Nature, vol. 461(7262), pages 393-398, September.
    • Handle: RePEc:nat:nature:v:461:y:2009:i:7262:d:10.1038_nature08358
    DOI: 10.1038/nature08358
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    Cited by:

    1. Yuxi Wang & Mingshan Li & Jiahan Ying & Jie Shen & Daolong Dou & Meizhen Yin & Stephen C. Whisson & Paul R. J. Birch & Shuo Yan & Xiaodan Wang, 2023. "High-efficiency green management of potato late blight by a self-assembled multicomponent nano-bioprotectant," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Zhichao Zhang & Xiaoyi Zhang & Yuan Tian & Liyuan Wang & Jingting Cao & Hui Feng & Kainan Li & Yan Wang & Suomeng Dong & Wenwu Ye & Yuanchao Wang, 2024. "Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Mark C. Derbyshire & Sylvain Raffaele, 2023. "Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Riao, Dao & Guga, Suri & Bao, Yongbin & Liu, Xingping & Tong, Zhijun & Zhang, Jiquan, 2023. "Non-overlap of suitable areas of agro-climatic resources and main planting areas is the main reason for potato drought disaster in Inner Mongolia, China," Agricultural Water Management, Elsevier, vol. 275(C).
    5. Felix Homma & Jie Huang & Renier A. L. van der Hoorn, 2023. "AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Hui Sheng & Congcong Ai & Cancan Yang & Chunyuan Zhu & Zhe Meng & Fengzhi Wu & Xiaodan Wang & Daolong Dou & Paul F. Morris & Xiuguo Zhang, 2024. "A conserved oomycete effector RxLR23 triggers plant defense responses by targeting ERD15La to release NbNAC68," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    7. Hannah B. Rappaport & Angela M. Oliverio, 2023. "Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Allison Coomber & Amanda Saville & Jean Beagle Ristaino, 2024. "Evolution of Phytophthora infestans on its potato host since the Irish potato famine," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    9. Yadira F. Ordóñez & Josué Ruano & Pamela Avila & Lennys Berutti & Paola Chavez Guerrero & Paola E. Ordóñez, 2023. "In Vitro Antimicrobial Activity of Plant Species against the Phytopathogens Ralstonia solanacearum , Phytophthora infestans , and Neopestalotiopsis javaensis," Agriculture, MDPI, vol. 13(10), pages 1-11, October.

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