The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
ABSTRACT Asian soybean rust, caused by Phakopsora pachyrhizi , is one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi ’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizi ’s genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.
Authors 55
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University of East Anglia · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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Brazilian Agricultural Research Corporation
Affiliation as printed
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
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Affiliation as printed
Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
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National Center for Genome Resources
Affiliation as printed
National Center for Genome Resources, Santa Fe, New Mexico, U.S.A
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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University of East Anglia · Brazilian Agricultural Research Corporation · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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Brazilian Agricultural Research Corporation
Affiliation as printed
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
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Universidade Tecnológica Federal do Paraná · Brazilian Agricultural Research Corporation
Affiliation as printed
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
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Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Interactions Arbres-Microorganismes · Université de Lorraine
Affiliation as printed
Université de Lorraine, INRAE, IAM, Nancy, France
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Affiliation as printed
Syngenta Jealott’s Hill Int. Research Centre, Bracknell Berkshire, U.K
Syngenta Jealott's Hill Int. Research Centre, Bracknell Berkshire, U.K
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National Center for Genome Resources
Affiliation as printed
National Center for Genome Resources, Santa Fe, New Mexico, U.S.A
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University of East Anglia · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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University of East Anglia · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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University of East Anglia · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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Aix-Marseille Université · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Biodiversité et Biotechnologie Fongiques · Architecture et Fonction des Macromolécules Biologiques
Affiliation as printed
AFMB, Aix-Marseille Univ., INRAE, Marseille, France
Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
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King Abdulaziz University · Technical University of Denmark
Affiliation as printed
DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Universidade Tecnológica Federal do Paraná · Brazilian Agricultural Research Corporation
Affiliation as printed
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Affiliation as printed
KeyGene N.V., Wageningen, The Netherlands
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Affiliation as printed
KeyGene N.V., Wageningen, The Netherlands
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Universidade Federal de Viçosa
Affiliation as printed
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Affiliation as printed
KeyGene N.V., Wageningen, The Netherlands
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Affiliation as printed
KeyGene N.V., Wageningen, The Netherlands
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Universidade Federal de Viçosa
Affiliation as printed
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Universidade Federal de Viçosa
Affiliation as printed
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Affiliation as printed
Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
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Affiliation as printed
Syngenta Crop Protection AG, Stein, Switzerland
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Lawrence Berkeley National Laboratory · Joint Genome Institute
Affiliation as printed
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Brazilian Agricultural Research Corporation
Affiliation as printed
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
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Affiliation as printed
Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
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Affiliation as printed
Syngenta Crop Protection, LLC, Research Triangle Park, North Carolina, U.S.A
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Lawrence Berkeley National Laboratory · Joint Genome Institute · University of California, Berkeley
Affiliation as printed
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, U.S.A
U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, U.S.A
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Universidade Federal de Viçosa
Affiliation as printed
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
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Affiliation as printed
Bayer SAS, Crop Science Division, Lyon, France
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Affiliation as printed
Syngenta Crop Protection AG, Stein, Switzerland
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Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Interactions Arbres-Microorganismes · Université de Lorraine
Affiliation as printed
Université de Lorraine, INRAE, IAM, Nancy, France
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H. Peter van Esse corresponding
University of East Anglia · Sainsbury Laboratory
Affiliation as printed
2Blades, Evanston, Illinois, U.S.A
The Sainsbury Laboratory, University of East Anglia, Norwich, U.K
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