Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

Yogesh K. Gupta, Francismar C. Marcelino-Guimarães, Cécile Lorrain, Andrew Farmer, Sajeet Haridas, Everton Geraldo Capote Ferreira, Valéria S. Lopes-Caitar, Liliane Santana Oliveira, Emmanuelle Morin, Stephanie Widdison, Connor Cameron, Yoshihiro Inoue, Kathrin Thor, Kelly Robinson, Elodie Drula, Bernard Henrissat, Kurt LaButti, Aline Mara Rudsit Bini, Eric Paget, Vasanth Singan, Christopher Daum, Cécile Dorme, Milan Hoek, Antoine Janssen, Lucie Chandat, Yannick Tarriotte, Jake Richardson, Bernardo do Vale Araújo Melo, Alexander H. J. Wittenberg, Harrie Schneiders, Stephane Peyrard, Larissa Goulart Zanardo, Valéria Cristina Holtman, Flavie Coulombier-Chauvel, Tobias I. Link, Dirk Balmer, André N. Müller, Sabine Kind, Stefan Bohnert, Louisa Wirtz, Cindy Chen, Mi Yan, Vivian Ng, Pierrick Gautier, Maurício Conrado Meyer, Ralf Thomas Voegele, Qingli Liu, Igor V. Grigoriev, Uwe Conrath, Sérgio H. Brommonschenkel, Marco Loehrer, Ulrich Schaffrath, Catherine Sirven, Gabriel Scalliet, Sébastien Duplessis and H. Peter Esse ()
Additional contact information
Yogesh K. Gupta: 2Blades
Francismar C. Marcelino-Guimarães: Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
Cécile Lorrain: ETH Zürich
Andrew Farmer: National Center for Genome Resources
Sajeet Haridas: Lawrence Berkeley National Laboratory
Everton Geraldo Capote Ferreira: 2Blades
Valéria S. Lopes-Caitar: Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
Liliane Santana Oliveira: Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
Emmanuelle Morin: Université de Lorraine, INRAE, IAM
Stephanie Widdison: Syngenta Jealott’s Hill Int. Research Centre
Connor Cameron: National Center for Genome Resources
Yoshihiro Inoue: 2Blades
Kathrin Thor: 2Blades
Kelly Robinson: 2Blades
Elodie Drula: AFMB, Aix-Marseille Univ., INRAE
Bernard Henrissat: King Abdulaziz University
Kurt LaButti: Lawrence Berkeley National Laboratory
Aline Mara Rudsit Bini: Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
Eric Paget: Bayer SAS, Crop Science Division
Vasanth Singan: Lawrence Berkeley National Laboratory
Christopher Daum: Lawrence Berkeley National Laboratory
Cécile Dorme: Bayer SAS, Crop Science Division
Milan Hoek: KeyGene N.V.
Antoine Janssen: KeyGene N.V.
Lucie Chandat: Bayer SAS, Crop Science Division
Yannick Tarriotte: Bayer SAS, Crop Science Division
Jake Richardson: The John Innes Centre
Bernardo do Vale Araújo Melo: Universidade Federal de Viçosa
Alexander H. J. Wittenberg: KeyGene N.V.
Harrie Schneiders: KeyGene N.V.
Stephane Peyrard: Bayer SAS, Crop Science Division
Larissa Goulart Zanardo: Universidade Federal de Viçosa
Valéria Cristina Holtman: Universidade Federal de Viçosa
Flavie Coulombier-Chauvel: Bayer SAS, Crop Science Division
Tobias I. Link: University of Hohenheim
Dirk Balmer: Syngenta Crop Protection AG
André N. Müller: RWTH Aachen University
Sabine Kind: RWTH Aachen University
Stefan Bohnert: RWTH Aachen University
Louisa Wirtz: RWTH Aachen University
Cindy Chen: Lawrence Berkeley National Laboratory
Mi Yan: Lawrence Berkeley National Laboratory
Vivian Ng: Lawrence Berkeley National Laboratory
Pierrick Gautier: Bayer SAS, Crop Science Division
Maurício Conrado Meyer: Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
Ralf Thomas Voegele: University of Hohenheim
Qingli Liu: Syngenta Crop Protection, LLC, Research Triangle Park
Igor V. Grigoriev: Lawrence Berkeley National Laboratory
Uwe Conrath: RWTH Aachen University
Sérgio H. Brommonschenkel: Universidade Federal de Viçosa
Marco Loehrer: RWTH Aachen University
Ulrich Schaffrath: RWTH Aachen University
Catherine Sirven: Bayer SAS, Crop Science Division
Gabriel Scalliet: Syngenta Crop Protection AG
Sébastien Duplessis: Université de Lorraine, INRAE, IAM
H. Peter Esse: 2Blades

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, 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. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

Date: 2023
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Citations: View citations in EconPapers (1)

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DOI: 10.1038/s41467-023-37551-4

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