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 (1, 2) , Bernard Henrissat , Kurt Labutti , Aline Mara Rudsit Bini , Eric Paget , Vasanth Singan , Christopher Daum , Cécile Dorme , Milan van 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 , H. Peter van Esse

1 BBF - Biodiversité et Biotechnologie Fongiques
2 AFMB - Architecture et fonction des macromolécules biologiques

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.

Domaines: Sciences du Vivant [q-bio]

Yogesh K Gupta, Francismar C Marcelino-Guimarães, Cécile Lorrain, Andrew Farmer, Sajeet Haridas, et al.. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nature Communications, 2023, 14 (1), pp.1835. ⟨10.1038/s41467-023-37551-4⟩. ⟨hal-04143167⟩