Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races

Yuanwen Guo, Bliss Betzen, Andres Salcedo, Fei He, Robert L. Bowden, John P. Fellers, Katherine W. Jordan, Alina Akhunova, Mathew N. Rouse, Les J. Szabo () and Eduard Akhunov ()
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Yuanwen Guo: Kansas State University
Bliss Betzen: Kansas State University
Andres Salcedo: Kansas State University
Fei He: Kansas State University
Robert L. Bowden: USDA-ARS, Hard Winter Wheat Genetics Research Unit
John P. Fellers: USDA-ARS, Hard Winter Wheat Genetics Research Unit
Katherine W. Jordan: Kansas State University
Alina Akhunova: Kansas State University
Mathew N. Rouse: University of Minnesota & USDA-ARS, Cereal Disease Lab
Les J. Szabo: University of Minnesota & USDA-ARS, Cereal Disease Lab
Eduard Akhunov: Kansas State University

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.

Date: 2022
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DOI: 10.1038/s41467-022-34050-w

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