Cecile Lorrain

Fungal regulatory genomics & evolution

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


Journal article


Yogesh K. Gupta, F. Marcelino-Guimarães, Cécile Lorrain, A. Farmer, S. Haridas, E. G. C. Ferreira, V. Lopes-Caitar, Liliane Santana Oliveira, E. Morin, Stephanie Widdison, Connor Cameron, Y. Inoue, Kathrin Thor, Kelly A. Robinson, E. Drula, B. Henrissat, K. Labutti, A. Bini, E. Paget, Vasanth R. Singan, Christopher Daum, Cécile Dorme, M. V. van Hoek, A. Janssen, Lucie Chandat, Y. Tarriotte, J. Richardson, B. D. V. A. Melo, A. Wittenberg, Harrie Schneiders, S. Peyrard, L. G. Zanardo, V. 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, M. C. Meyer, R. Voegele, Qingli Liu, I. Grigoriev, U. Conrath, S. Brommonschenkel, M. Loehrer, U. Schaffrath, C. Sirven, G. Scalliet, S. Duplessis, H. P. van Esse
Nature Communications, 2023

Semantic Scholar DOI PubMedCentral PubMed
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APA   Click to copy
Gupta, Y. K., Marcelino-Guimarães, F., Lorrain, C., Farmer, A., Haridas, S., Ferreira, E. G. C., … van Esse, H. P. (2023). Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nature Communications.


Chicago/Turabian   Click to copy
Gupta, Yogesh K., F. Marcelino-Guimarães, Cécile Lorrain, A. Farmer, S. Haridas, E. G. C. Ferreira, V. Lopes-Caitar, et al. “Major Proliferation of Transposable Elements Shaped the Genome of the Soybean Rust Pathogen Phakopsora Pachyrhizi.” Nature Communications (2023).


MLA   Click to copy
Gupta, Yogesh K., et al. “Major Proliferation of Transposable Elements Shaped the Genome of the Soybean Rust Pathogen Phakopsora Pachyrhizi.” Nature Communications, 2023.


BibTeX   Click to copy

@article{yogesh2023a,
  title = {Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi},
  year = {2023},
  journal = {Nature Communications},
  author = {Gupta, Yogesh K. and Marcelino-Guimarães, F. and Lorrain, Cécile and Farmer, A. and Haridas, S. and Ferreira, E. G. C. and Lopes-Caitar, V. and Oliveira, Liliane Santana and Morin, E. and Widdison, Stephanie and Cameron, Connor and Inoue, Y. and Thor, Kathrin and Robinson, Kelly A. and Drula, E. and Henrissat, B. and Labutti, K. and Bini, A. and Paget, E. and Singan, Vasanth R. and Daum, Christopher and Dorme, Cécile and van Hoek, M. V. and Janssen, A. and Chandat, Lucie and Tarriotte, Y. and Richardson, J. and Melo, B. D. V. A. and Wittenberg, A. and Schneiders, Harrie and Peyrard, S. and Zanardo, L. G. and Holtman, V. and Coulombier-Chauvel, Flavie and Link, Tobias I. and Balmer, Dirk and Müller, André N. and Kind, Sabine and Bohnert, Stefan and Wirtz, Louisa and Chen, Cindy and Yan, Mi and Ng, Vivian and Gautier, Pierrick and Meyer, M. C. and Voegele, R. and Liu, Qingli and Grigoriev, I. and Conrath, U. and Brommonschenkel, S. and Loehrer, M. and Schaffrath, U. and Sirven, C. and Scalliet, G. and Duplessis, S. and van Esse, H. P.}
}

Abstract

Asian soybean rust caused by Phakopsora pachyrhizi is an important plant pathogen, but an accurate genome assembly for this fungus has been lacking. This study sequenced three independent P. pachyrhizi isolates and generated reference quality assemblies and genome annotations, representing a critical step for further in-depth studies of this pathogen and the development of new methods of control. 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.


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