A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Alice Feurtey, Cécile Lorrain, Megan C. McDonald, Andrew Milgate, Peter S. Solomon, Rachael Warren, Guido Puccetti, Gabriel Scalliet, Stefano F. F. Torriani, Lilian Gout, Thierry C. Marcel, Frédéric Suffert, Julien Alassimone, Anna Lipzen, Yuko Yoshinaga, Christopher Daum, Kerrie Barry, Igor V. Grigoriev, Stephen B. Goodwin, Anne Genissel, Michael F. Seidl, Eva H. Stukenbrock, Marc-Henri Lebrun, Gert H. J. Kema, Bruce A. McDonald and Daniel Croll ()
Additional contact information
Alice Feurtey: University of Neuchâtel
Cécile Lorrain: Plant Pathology, D-USYS, ETH Zurich
Megan C. McDonald: The Australian National University
Andrew Milgate: Wagga Wagga Agricultural Institute
Peter S. Solomon: The Australian National University
Rachael Warren: The New Zealand Institute for Plant and Food Research Limited
Guido Puccetti: University of Neuchâtel
Gabriel Scalliet: Syngenta Crop Protection AG
Stefano F. F. Torriani: Syngenta Crop Protection AG
Lilian Gout: Université Paris Saclay, INRAE, UR BIOGER
Thierry C. Marcel: Université Paris Saclay, INRAE, UR BIOGER
Frédéric Suffert: Université Paris Saclay, INRAE, UR BIOGER
Julien Alassimone: Plant Pathology, D-USYS, ETH Zurich
Anna Lipzen: Lawrence Berkeley National Laboratory
Yuko Yoshinaga: Lawrence Berkeley National Laboratory
Christopher Daum: Lawrence Berkeley National Laboratory
Kerrie Barry: Lawrence Berkeley National Laboratory
Igor V. Grigoriev: Lawrence Berkeley National Laboratory
Stephen B. Goodwin: USDA-Agricultural Research Service
Anne Genissel: Université Paris Saclay, INRAE, UR BIOGER
Michael F. Seidl: Laboratory of Phytopathology
Eva H. Stukenbrock: Max Planck Institute for Evolutionary Biology
Marc-Henri Lebrun: Université Paris Saclay, INRAE, UR BIOGER
Gert H. J. Kema: Laboratory of Phytopathology
Bruce A. McDonald: Plant Pathology, D-USYS, ETH Zurich
Daniel Croll: University of Neuchâtel

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: 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 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.

Date: 2023
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DOI: 10.1038/s41467-023-36674-y

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