TY - JOUR
T1 - Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi
AU - Gupta, Yogesh K.
AU - Marcelino-Guimarães, Francismar C.
AU - Lorrain, Cécile
AU - Farmer, Andrew
AU - Haridas, Sajeet
AU - Ferreira, Everton Geraldo Capote
AU - Lopes-Caitar, Valéria S.
AU - Oliveira, Liliane Santana
AU - Morin, Emmanuelle
AU - Widdison, Stephanie
AU - Cameron, Connor
AU - Inoue, Yoshihiro
AU - Thor, Kathrin
AU - Robinson, Kelly
AU - Drula, Elodie
AU - Henrissat, Bernard
AU - LaButti, Kurt
AU - Bini, Aline Mara Rudsit
AU - Paget, Eric
AU - Singan, Vasanth
AU - Daum, Christopher
AU - Dorme, Cécile
AU - van Hoek, Milan
AU - Janssen, Antoine
AU - Chandat, Lucie
AU - Tarriotte, Yannick
AU - Richardson, Jake
AU - Melo, Bernardo do Vale Araújo
AU - Wittenberg, Alexander H.J.
AU - Schneiders, Harrie
AU - Peyrard, Stephane
AU - Zanardo, Larissa Goulart
AU - Holtman, Valéria Cristina
AU - Coulombier-Chauvel, Flavie
AU - Link, Tobias I.
AU - Balmer, Dirk
AU - Müller, André N.
AU - Kind, Sabine
AU - Bohnert, Stefan
AU - Wirtz, Louisa
AU - Chen, Cindy
AU - Yan, Mi
AU - Ng, Vivian
AU - Gautier, Pierrick
AU - Meyer, Maurício Conrado
AU - Voegele, Ralf Thomas
AU - Liu, Qingli
AU - Grigoriev, Igor V.
AU - Conrath, Uwe
AU - Brommonschenkel, Sérgio H.
AU - Loehrer, Marco
AU - Schaffrath, Ulrich
AU - Sirven, Catherine
AU - Scalliet, Gabriel
AU - Duplessis, Sébastien
AU - van Esse, H. Peter
N1 - 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).
PY - 2023/4/1
Y1 - 2023/4/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85151327035&partnerID=8YFLogxK
U2 - 10.1038/s41467-023-37551-4
DO - 10.1038/s41467-023-37551-4
M3 - Article
C2 - 37005409
AN - SCOPUS:85151327035
SN - 2041-1723
VL - 14
JO - Nature Communications
JF - Nature Communications
M1 - 1835
ER -