Abstract
Wheat stem rust is a disease of global importance caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt). Here we generate chromosome-level, nuclear-phased genome references for Pgt isolates ETH2013-1 and ITA2018-1, representing races TKTTF and TTRTF respectively, that have caused major epidemics in Africa and Europe. The nuclear haplotypes of ETH2013-1 and ITA2018-1 are unique and unrelated to those of Ug99 and Pgt21. Pgt nuclear haplotypes show extensive variation in sequence and copy number of six known Avr genes and AvrSr33, which we identify through an effector gene library screen. Recognition properties of 22 novel Avr gene variants explain the race virulence phenotypes and the outbreak of TTRTF on durum cultivars containing Sr13b, since ITA2018-1 carries a homozygous deletion of AvrSr13. This work establishes an Avr gene atlas for Pgt that can inform wheat breeding and enable development of sequence-based virulence diagnostic tools for pathogen surveillance.
Data availability
All raw sequence data are available under NCBI BioProject PRJNA1267768. Assembly and annotation files are deposited in the CSIRO data access portal (https://data.csiro.au/collection/csiro:65828). Source data are provided with this paper.
Code availability
Scripts are available at https://github.com/henni164/epidemic_pgt (Zenodo https://doi.org/10.5281/zenodo.18322261).
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Acknowledgements
This project was supported by USDA-NIFA award 2022-67013-36505 to BJS and BBSRC grant BB/W018403/1 to KK as part of the NSF/BBSRC Lead Agency Agreement, the CSIRO Research Office to JS, PND and MF (OD-227545, OD-235285), the CSIRO Synthetic Biology Future Science Platform to TV (OD-213047), the Grains Research and Development Corporation project CSP2403-014RTX to PND, the Lieberman-Okinow Endowment at the University of Minnesota to BJS, the 2Blades Foundation to MF and the Gatsby Foundation to PND, MA, MF. ECH was supported by an ANU University Research Scholarship and an ANU/CSIRO Digital Agriculture PhD Supplementary Scholarship. We acknowledge Dr David Hodson at CIMMYT for providing the rust isolate ETH2013-1, as well as Dr Matthew J Moscou and Kim-Phuong Nguyen for discussions and feedback as well as technical support. We truly appreciate their unwavering support. We thank Stephanie Dahl and Aubree Kees for their assistance at the University of Minnesota Biosafety Level-3 containment facility, the Minnesota Supercomputing Institute, and CSIRO High Performance Computing Services for computational resources, and Peter Tyson and Joel Hansen for providing computational support. We thank Biagio Randazzo (AS.A.R. - Società Semplice Agricola Randazzo, Baucina (PA), Italy) and Massimo Palumbo (CREA - Council for Agricultural Research and Economics, Research Center for Cereal and Industrial Crops, Acireale (CT), Italy) for their involvement in processing the rust isolate ITA2018-1.
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Conceptualization: K.K., P.N.D., B.J.S., M.F.; Data curation: R.S., E.C.H., C.L.P., J.S.; Formal analysis: R.S., E.C.H., C.L.P., J.C., J.L., O.M., J.S.; Investigation: R.S., E.C.H., C.L.P., J.C., J.L., O.M., D.L., L.C.C., Z.S., A.F., E.S.N., F.L., M.A.O.; Project Administration: R.S., C.L.P., P.N.D., B.J.S., M.F.; Software: R.S., E.C.H., J.S.; Methodology: E.C.H., C.L.P., J.L., M.A.O., T.A., T.V., K.K., J.S., P.N.D., B.J.S., M.F.; Visualization: R.S., E.C.H., C.L.P., J.C., J.L., O.M.; Validation: C.L.P., J.C.; Writing – original draft: R.S., E.C.H., C.L.P., J.S., P.N.D., M.F.; Writing – review & editing: R.S., E.C.H., C.L.P., J.C., J.L., O.M., D.L., L.C.C., Z.S., A.F., E.S.N., F.L., M.A.O., T.A., T.V., N.V., M.L., M.A., E.S., K.K., J.S., P.N.D., B.J.S., M.F.; Resources: T.A., T.V., N.V., M.L., M.A., B.J.S.; Supervision: C.L.P., J.C., M.A.O., T.V., E.S., K.K., J.S., P.N.D., B.J.S., M.F.; Funding Acquisition: E.S., K.K., P.N.D., B.J.S., M.F.
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T.A, T.V., P.N.D., M.F., and J.S. are inventors on patent application WO2024103117 filed by CSIRO and relating to the identification of protein-protein interactions by protoplast screening. The remaining authors declare that they have no competing interests.
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Spanner, R.E., Henningsen, E.C., Langlands-Perry, C. et al. Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69508-8
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DOI: https://doi.org/10.1038/s41467-026-69508-8
