A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
Feurtey, Alice; Lorrain, Cécile; McDonald, Megan C; Milgate, Andrew; Solomon, Peter S; Warren, Rachael; Puccetti, Guido; Scalliet, Gabriel; Torriani, Stefano F F; Gout, Lilian; Marcel, Thierry C; Suffert, Frédéric; Alassimone, Julien; Lipzen, Anna; Yoshinaga, Yuko; Daum, Christopher; Barry, Kerrie; Grigoriev, Igor V; Goodwin, Stephen B; Genissel, Anne; Seidl, Michael F; Stukenbrock, Eva H; Lebrun, Marc-Henri; Kema, Gert H J; McDonald, Bruce A; Croll, Daniel
(2023) Nature Communications, volume 14, issue 1
(Article)
Abstract
Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of
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crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.
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Keywords: Humans, Adaptation, Physiological, Virulence/genetics, Acclimatization, Genomics, Plant Diseases/microbiology, Resistance, Mycosphaerella-graminicola, Populations, Genes, Plant-pathogens, General Physics and Astronomy, General Chemistry, General Biochemistry,Genetics and Molecular Biology
ISSN: 2041-1723
Publisher: Nature Publishing Group
Note: Funding Information: Data produced and analyzed in this paper were generated in collaboration with the Genetic Diversity Centre (GDC), ETH Zurich. We would like to thank Lucio Garcia and the NGS platform at Syngenta for assistance with sequencing. DC and GS were supported by the Swiss Innovation Agency Innosuisse. The work (proposal: 10.46936/10.25585/60000699) 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 operated under Contract No. DE-AC02-05CH11231 and lab work was supported by the USDA-Agricultural Research Service project 3602-22000-015-00D. AF was supported by a grant from the DFG priority programme SPP1819 awarded to EHS. Funding Information: Data produced and analyzed in this paper were generated in collaboration with the Genetic Diversity Centre (GDC), ETH Zurich. We would like to thank Lucio Garcia and the NGS platform at Syngenta for assistance with sequencing. DC and GS were supported by the Swiss Innovation Agency Innosuisse. The work (proposal: 10.46936/10.25585/60000699) 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 operated under Contract No. DE-AC02-05CH11231 and lab work was supported by the USDA-Agricultural Research Service project 3602-22000-015-00D. AF was supported by a grant from the DFG priority programme SPP1819 awarded to EHS. Publisher Copyright: © 2023, The Author(s).
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