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ToolsGupta, 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 and van Esse, H. Peter (2023) Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nature Communications, 14. ISSN 2041-1723
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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.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability statement: Source data are provided with this paper. The raw sequencing data of MT2006, K8108 and UFV02 isolates has been deposited at NCBI under the accession numbers PRJNA368291, PRJEB46918, and PRJEB44222, respectively. Source data are provided with this paper. Funding Information: The work (Proposal 10.46936/10.25585/60000959) conducted by the U.S. Department of Energy Joint Genome Institute. (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Sequencing and RNAseq analyses of UFV02 was supported by 2Blades. Work on the soybean isolate K8108 in the Conrath and Schaffrath lab was supported, in part, by Syngenta Crop Protection. EM, CL and SD were in part funded by the Labex Arbre (Programme Investissement d’Avenir, ANR-11-LABX-0002-01). |
| Uncontrolled Keywords: | chemistry(all),biochemistry, genetics and molecular biology(all),physics and astronomy(all) ,/dk/atira/pure/subjectarea/asjc/1600 |
| Faculty \ School: | Faculty of Science > The Sainsbury Laboratory Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2024 14:30 |
| Last Modified: | 01 Nov 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97223 |
| DOI: | 10.1038/s41467-023-37551-4 |
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