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

Gupta, Yogesh K.; Marcelino-Guimarães, Francismar C.; Lorrain, Cécile; Farmer, Andrew; Haridas, Sajeet; Ferreira, Everton Geraldo Capote; Lopes-Caitar, Valéria S.; Oliveira, Liliane Santana; Morin, Emmanuelle; Widdison, Stephanie; Cameron, Connor; Inoue, Yoshihiro; Thor, Kathrin; Robinson, Kelly; Drula, Elodie; Henrissat, Bernard; LaButti, Kurt; Bini, Aline Mara Rudsit; Paget, Eric; Singan, Vasanth; Daum, Christopher; Dorme, Cécile; van Hoek, Milan; Janssen, Antoine; Chandat, Lucie; Tarriotte, Yannick; Richardson, Jake; Melo, Bernardo do Vale Araújo; Wittenberg, Alexander H. J.; Schneiders, Harrie; Peyrard, Stephane; Zanardo, Larissa Goulart; Holtman, Valéria Cristina; Coulombier-Chauvel, Flavie; Link, Tobias I.; Balmer, Dirk; Müller, André N.; Kind, Sabine; Bohnert, Stefan; Wirtz, Louisa; Chen, Cindy; Yan, Mi; Ng, Vivian; Gautier, Pierrick; Meyer, Maurício Conrado; Voegele, Ralf Thomas; Liu, Qingli; Grigoriev, Igor V.; Conrath, Uwe; Brommonschenkel, Sérgio H.; Loehrer, Marco; Schaffrath, Ulrich; Sirven, Catherine; Scalliet, Gabriel; Duplessis, Sébastien; van Esse, H. Peter

doi:10.1038/s41467-023-37551-4

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

Journal Article · Sat Apr 01 00:00:00 EDT 2023 · Nature Communications

DOI:https://doi.org/10.1038/s41467-023-37551-4· OSTI ID:2228613

^[1]; ^[2]; ^[3]; Farmer, Andrew ^[4]; ^[5]; ^[6]; ^[2]; Oliveira, Liliane Santana ^[7]; Morin, Emmanuelle ^[8]; Widdison, Stephanie ^[9]; Cameron, Connor ^[4]; Inoue, Yoshihiro ^[1]; Thor, Kathrin ^[1]; Robinson, Kelly ^[1]; ^[10]; ^[11]; ^[5]; Bini, Aline Mara Rudsit ^[7]; Paget, Eric ^[12]; Singan, Vasanth ^[5] more »

2Blades, Evanston, IL (United States); University of East Anglia, Norwich (United Kingdom)
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná (Brazil)
Eidgenoessische Technische Hochschule (ETH), Zurich (Switzerland)
National Center for Genome Resources, Santa Fe, NM (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). USDOE Joint Genome Institute
2Blades, Evanston, IL (United States); University of East Anglia, Norwich (United Kingdom); Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná (Brazil)
Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná (Brazil); Federal University of Technology of Paraná (UTFPR) (Brazil)
Université de Lorraine, INRAE, IAM, Nancy (France)
Syngenta Jealott’s Hill International Research Centre, Bracknell (United Kingdom)
AFMB, Aix-Marseille Université, INRAE (France); Biodiversité et Biotechnologie Fongiques, INRAE, Marseille (France)
King Abdulaziz University, Jeddah (Saudi Arabia); Technical University of Denmark, Lyngby (Denmark)
Bayer SAS, Lyon (France). Crop Science Division
KeyGene N.V., Wageningen (Netherlands)
The John Innes Centre, Norwich (United Kingdom)
Universidade Federal de Viçosa (Brazil)
University of Hohenheim, Stuttgart (Germany)
Syngenta Crop Protection AG, Stein (Switzerland)
RWTH Aachen University (Germany)
Syngenta Crop Protection, LLC, Durham, NC (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). USDOE Joint Genome Institute; University of California, Berkeley, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2228613

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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