Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi
Yogesh K. Gupta, Francismar Corrêa Marcelino‐Guimarães, Cécile Lorrain, Andrew Farmer, Sajeet Haridas, Everton Geraldo Capote Ferreira, Valéria Stefania Lopes-Caitar, Liliane Santana Oliveira, Emmanuelle Morin, Stephanie Widdison, Connor Cameron, Yoshihiro Inoue, Kathrin Thor, Kelly Robinson, Élodie Drula, Bernard Henrissat, Kurt LaButti, Aline Mara Rudsit Bini, Eric Paget, Vasanth Singan, Chris Daum, Cécile Dorme, Milan van Hoek, Antoine Janssen, Lucie Chandat, Yannick Tarriotte, J. Steven Richardson, Bernardo do Vale Araújo Melo, Alexander Wittenberg, Harrie Schneiders, Stephane Peyrard, Larissa G. Zanardo, Valéria Cristina Holtman, Flavie Coulombier-Chauvel, Tobias Link, Dirk Balmer, André N. Müller, Sabine Kind, Stefan Bohnert, Louisa Wirtz, Cindy Chen, Mi Yan, Vivian Ng, Pierrick Gautier, M. C. Meyer, Ralf T. Voegele, Qingli Liu, Igor V. Grigoriev, Uwe Conrath, Sérgio Hermínio Brommonschenkel, Marco Loehrer, Ulrich Schaffrath, Catherine Sirven, Gabriel Scalliet, Sébastien Duplessis, H. Peter van Esse
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.