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

Autor: Gupta YK; 2Blades, Evanston, Illinois, USA.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK., Marcelino-Guimarães FC; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil., Lorrain C; Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland., Farmer A; National Center for Genome Resources, Santa Fe, New Mexico, USA., Haridas S; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Ferreira EGC; 2Blades, Evanston, Illinois, USA.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK.; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil., Lopes-Caitar VS; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil., Oliveira LS; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.; Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil., Morin E; Université de Lorraine, INRAE, IAM, Nancy, France., Widdison S; Syngenta Jealott's Hill Int. Research Centre, Bracknell Berkshire, UK., Cameron C; National Center for Genome Resources, Santa Fe, New Mexico, USA., Inoue Y; 2Blades, Evanston, Illinois, USA.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK., Thor K; 2Blades, Evanston, Illinois, USA.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK., Robinson K; 2Blades, Evanston, Illinois, USA.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK., Drula E; AFMB, Aix-Marseille Univ., INRAE, Marseille, France.; Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France., Henrissat B; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.; DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark., LaButti K; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Bini AMR; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil.; Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil., Paget E; Bayer SAS, Crop Science Division, Lyon, France., Singan V; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Daum C; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Dorme C; Bayer SAS, Crop Science Division, Lyon, France., van Hoek M; KeyGene N.V., Wageningen, The Netherlands., Janssen A; KeyGene N.V., Wageningen, The Netherlands., Chandat L; Bayer SAS, Crop Science Division, Lyon, France., Tarriotte Y; Bayer SAS, Crop Science Division, Lyon, France., Richardson J; The John Innes Centre, Norwich, UK., Melo BDVA; Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil., Wittenberg AHJ; KeyGene N.V., Wageningen, The Netherlands., Schneiders H; KeyGene N.V., Wageningen, The Netherlands., Peyrard S; Bayer SAS, Crop Science Division, Lyon, France., Zanardo LG; Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil., Holtman VC; Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil., Coulombier-Chauvel F; Bayer SAS, Crop Science Division, Lyon, France., Link TI; Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany., Balmer D; Syngenta Crop Protection AG, Stein, Switzerland., Müller AN; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Kind S; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Bohnert S; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Wirtz L; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Chen C; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Yan M; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Ng V; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Gautier P; Bayer SAS, Crop Science Division, Lyon, France., Meyer MC; Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil., Voegele RT; Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany., Liu Q; Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA., Grigoriev IV; U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA., Conrath U; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Brommonschenkel SH; Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil., Loehrer M; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Schaffrath U; Department of Plant Physiology, RWTH Aachen University, Aachen, Germany., Sirven C; Bayer SAS, Crop Science Division, Lyon, France., Scalliet G; Syngenta Crop Protection AG, Stein, Switzerland., Duplessis S; Université de Lorraine, INRAE, IAM, Nancy, France., van Esse HP; 2Blades, Evanston, Illinois, USA. Peter.vanesse@tsl.ac.uk.; The Sainsbury Laboratory, University of East Anglia, Norwich, UK. Peter.vanesse@tsl.ac.uk.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2023 Apr 01; Vol. 14 (1), pp. 1835. Date of Electronic Publication: 2023 Apr 01.
DOI: 10.1038/s41467-023-37551-4
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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