ArticleNature communications2023
Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi.
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Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27citing papers in PubMed
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27 citing papers in PubMed, 53 citations in OpenAlex.
- A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy.G3 (Bethesda, Md.) · 2026Article
- Haplotype-phased genomes of the barley leaf rust pathogen reveal evidence of repeat element expansion and somatic hybridization.G3 (Bethesda, Md.) · 2026Article
- Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry.The New phytologist · 2026Article
- The conserved nematode pheromone ascr#18 primes plant immunity.Communications biology · 2026Article
- Comparative genome analysis identifies necrosis-inducing effectors in the lentil pathogen Ascochyta lentis in isolates with distinct virulence profiles.BMC genomics · 2026Article
- Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Integrative multi-omics analysis reveals stress-specific molecular architectures in soybean under drought and rust infection.BMC genomics · 2026Article
- Avirulence genes identified through linkage mapping and region-specific association studies in the wheat leaf rust pathogen Puccinia triticina.BMC genomics · 2026Article
- Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen.BMC biology · 2025Article
- A genomic perspective on fungal diversity and evolution.Nature reviews. Microbiology · 2025Review
- Temporal proteomic profiling via 4D-DIA reveals early defense mechanisms and core resistance determinants in soybean against Phakopsora pachyrhizi.Stress biology · 2025Article
- Ultrastructural Examination of the Fungus-To-Fungus Interactions ofPlant-environment interactions (Hoboken, N.J.) · 2025Article
- Population Genomics Reveals Distinct Lineage of the Asian Soybean Rust Fungus Phakopsora pachyrhizi in the United States of America Unrelated to Brazilian Populations.Molecular plant pathology · 2025Article
- Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi.BMC genomics · 2025Article
- Spatial and single-cell transcriptomics capture two distinct cell states in soybean defense response toFrontiers in plant science · 2025Article
- Soybean genomics research community strategic plan: A vision for 2024-2028.The plant genome · 2024Article
- Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini.Molecular plant pathology · 2024Article
- Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review.Plants (Basel, Switzerland) · 2024Review
- Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association.BMC plant biology · 2024Article
- Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment ineLife · 2024Article
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Authors and funding
56 authors at 18 institutions in 9 countries.
Yogesh K Gupta2Blades, Evanston, Illinois, USA.ORCID 0000-0002-8696-9044
Francismar C Marcelino-GuimarãesBrazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.ORCID 0000-0002-5828-7249
Cécile LorrainPathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland.ORCID 0000-0001-9727-2616
Andrew FarmerNational Center for Genome Resources, Santa Fe, New Mexico, USA.
Sajeet HaridasU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-0229-0975
Everton Geraldo Capote Ferreira2Blades, Evanston, Illinois, USA.ORCID 0000-0003-3326-5876
Valéria S Lopes-CaitarBrazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.ORCID 0000-0002-6204-0716
Liliane Santana OliveiraBrazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.
Emmanuelle MorinUniversité de Lorraine, INRAE, IAM, Nancy, France.
Stephanie WiddisonSyngenta Jealott's Hill Int. Research Centre, Bracknell Berkshire, UK.
Connor CameronNational Center for Genome Resources, Santa Fe, New Mexico, USA.
Yoshihiro Inoue2Blades, Evanston, Illinois, USA.
Kathrin Thor2Blades, Evanston, Illinois, USA.
Kelly Robinson2Blades, Evanston, Illinois, USA.
Elodie DrulaAFMB, Aix-Marseille Univ., INRAE, Marseille, France.ORCID 0000-0002-9168-5214
Bernard HenrissatDepartment of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.ORCID 0000-0002-3434-8588
Kurt LaButtiU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-5838-1972
Aline Mara Rudsit BiniBrazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.
Eric PagetBayer SAS, Crop Science Division, Lyon, France.
Vasanth SinganU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Christopher DaumU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Cécile DormeBayer SAS, Crop Science Division, Lyon, France.
Milan van HoekKeyGene N.V., Wageningen, The Netherlands.
Antoine JanssenKeyGene N.V., Wageningen, The Netherlands.
Lucie ChandatBayer SAS, Crop Science Division, Lyon, France.
Yannick TarriotteBayer SAS, Crop Science Division, Lyon, France.
Jake RichardsonThe John Innes Centre, Norwich, UK.
Bernardo do Vale Araújo MeloDepartamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil.
Alexander H J WittenbergKeyGene N.V., Wageningen, The Netherlands.
Harrie SchneidersKeyGene N.V., Wageningen, The Netherlands.
Stephane PeyrardBayer SAS, Crop Science Division, Lyon, France.ORCID 0000-0001-7146-8100
Larissa Goulart ZanardoDepartamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil.
Valéria Cristina HoltmanDepartamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil.
Flavie Coulombier-ChauvelBayer SAS, Crop Science Division, Lyon, France.
Tobias I LinkInstitute of Phytomedicine, University of Hohenheim, Stuttgart, Germany.
Dirk BalmerSyngenta Crop Protection AG, Stein, Switzerland.
André N MüllerDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.
Sabine KindDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.ORCID 0000-0003-2356-9382
Stefan BohnertDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.
Louisa WirtzDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.
Cindy ChenU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Mi YanU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Vivian NgU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0001-8941-6931
Pierrick GautierBayer SAS, Crop Science Division, Lyon, France.ORCID 0000-0002-6768-3112
Maurício Conrado MeyerBrazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.ORCID 0000-0001-5751-1715
Ralf Thomas VoegeleInstitute of Phytomedicine, University of Hohenheim, Stuttgart, Germany.ORCID 0000-0002-6068-8244
Qingli LiuSyngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA.
Igor V GrigorievU.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-3136-8903
Uwe ConrathDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.ORCID 0000-0002-8503-1943
Sérgio H BrommonschenkelDepartamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil.
Marco LoehrerDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.ORCID 0000-0002-3740-0855
Ulrich SchaffrathDepartment of Plant Physiology, RWTH Aachen University, Aachen, Germany.ORCID 0000-0002-3691-0888
Catherine SirvenBayer SAS, Crop Science Division, Lyon, France.
Gabriel Scalliet *Syngenta Crop Protection AG, Stein, Switzerland.ORCID 0000-0002-7291-2522
Sébastien Duplessis *Université de Lorraine, INRAE, IAM, Nancy, France.ORCID 0000-0002-2072-2989
H Peter van Esse *2Blades, Evanston, Illinois, USA. Peter.vanesse@tsl.ac.uk.ORCID 0000-0002-3667-060X
Bayer (France) · FRLawrence Berkeley National Laboratory · USRWTH Aachen University · DEUniversity of East Anglia · GBKeyGene (Netherlands) · NLUniversidade Federal de Viçosa · BRBrazilian Agricultural Research Corporation · BRInstitut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · FRNational Center for Genome Resources · USSyngenta (Switzerland) · CHUniversidade Tecnológica Federal do Paraná · BRUniversity of Hohenheim · DEAix-Marseille Université · FRETH Zurich · CHJohn Innes Centre · GBKing Abdulaziz University · SASyngenta (United Kingdom) · GBSyngenta (United States) · US
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
BasidiomycotaPhakopsora pachyrhiziCell ProliferationDNA Transposable ElementsEcosystemGlycine maxDNA Transposable Elements
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