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

Author

Listed:
  • Yogesh K. Gupta

    (2Blades
    University of East Anglia)

  • 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
    University of East Anglia
    Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja))

  • 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)
    Federal University of Technology of Paraná (UTFPR))

  • 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
    University of East Anglia)

  • Kathrin Thor

    (2Blades
    University of East Anglia)

  • Kelly Robinson

    (2Blades
    University of East Anglia)

  • Elodie Drula

    (AFMB, Aix-Marseille Univ., INRAE
    Biodiversité et Biotechnologie Fongiques, INRAE)

  • Bernard Henrissat

    (King Abdulaziz University
    Technical University of Denmark, Kgs)

  • Kurt LaButti

    (Lawrence Berkeley National Laboratory)

  • Aline Mara Rudsit Bini

    (Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja)
    Federal University of Technology of Paraná (UTFPR))

  • 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
    University of California Berkeley)

  • 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
    University of East Anglia)

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.

Suggested Citation

  • Yogesh K. Gupta & Francismar C. Marcelino-Guimarães & Cécile Lorrain & Andrew Farmer & Sajeet Haridas & Everton Geraldo Capote Ferreira & Valéria S. Lopes-Caitar & Liliane Santana Oliveira & Emmanuell, 2023. "Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37551-4
    DOI: 10.1038/s41467-023-37551-4
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    1. Qingnan Hao & Hongli Yang & Shuilian Chen & Chanjuan Zhang & Limiao Chen & Dong Cao & Songli Yuan & Wei Guo & Zhonglu Yang & Yi Huang & Yanhui Qu & Lucy Qin & Xiaoyan Sheng & Xueyan Wang & Chandrani M, 2024. "A pair of atypical NLR-encoding genes confers Asian soybean rust resistance in soybean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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