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Sperschneider J, Hewitt T, Lewis DC, Periyannan S, Milgate AW, Hickey LT, Mago R, Dodds PN, Figueroa M. Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina. Nat Microbiol 2023; 8:2130-2141. [PMID: 37884814 PMCID: PMC10627818 DOI: 10.1038/s41564-023-01494-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult to detect due to the lack of genome resolution between the two haploid nuclei. We examined three nuclear-phased genome assemblies of Puccinia triticina, which causes wheat leaf rust disease. We found that the most recently emerged Australian lineage was derived by nuclear exchange between two pre-existing lineages, which originated in Europe and North America. Haplotype-specific phylogenetic analysis reveals that repeated somatic exchange events have shuffled haploid nuclei between long-term clonal lineages, leading to a global P. triticina population representing different combinations of a limited number of haploid genomes. Thus, nuclear exchange seems to be the predominant mechanism generating diversity and the emergence of new strains in this otherwise clonal pathogen. Such genomics-accelerated surveillance of pathogen evolution paves the way for more accurate global disease monitoring.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - David C Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Sambasivam Periyannan
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
- School of Agriculture and Environmental Science, Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, New South Wales, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, GPO, Canberra, Australian Capital Territory, Australia.
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Wang C, Milgate AW, Solomon PS, McDonald MC. The identification of a transposon affecting the asexual reproduction of the wheat pathogen Zymoseptoria tritici. Mol Plant Pathol 2021; 22:800-816. [PMID: 33949756 PMCID: PMC8232023 DOI: 10.1111/mpp.13064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a fungal wheat pathogen that causes significant global yield losses. Within Z. tritici populations, quantitative differences in virulence among different isolates are commonly observed; however, the genetic components that underpin these differences remain elusive. In this study, intraspecific comparative transcriptomic analysis was used to identify candidate genes that contribute to differences in virulence on the wheat cultivar WW2449. This led to the identification of a multicopy gene that was not expressed in the high-virulence isolate when compared to the medium- and low-virulence isolates. Further investigation suggested this gene resides in a 7.9-kb transposon. Subsequent long-read sequencing of the isolates used in the transcriptomic analysis confirmed that this gene did reside in an active Class II transposon, which is composed of four genes named REP9-1 to -4. Silencing and overexpression of REP9-1 in two distinct genetic backgrounds demonstrated that its expression alone reduces the number of pycnidia produced by Z. tritici during infection. The REP9-1 gene identified within a Class II transposon is the first discovery of a gene in a transposable element that influences the virulence of Z. tritici. This discovery adds further complexity to genetic loci that contribute to quantitative virulence in this important pathogen.
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Affiliation(s)
- Chen Wang
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Andrew W. Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSWAustralia
| | - Peter S. Solomon
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Megan C. McDonald
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamUK
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Yang N, McDonald MC, Solomon PS, Milgate AW. Genetic mapping of Stb19, a new resistance gene to Zymoseptoria tritici in wheat. Theor Appl Genet 2018; 131:2765-2773. [PMID: 30238255 DOI: 10.1007/s00122-018-3189-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/10/2018] [Indexed: 05/26/2023]
Abstract
A new and dominant R gene Stb19 is identified from a soft wheat cultivar 'Lorikeet' and was mapped on the distal region of chromosome 1DS. Two tightly linked KASP markers were also discovered and validated for molecular-assisted breeding programs. A new R gene, designated as Stb19, provides resistance to Zymoseptoria tritici in wheat. This new dominant gene resides on the short arm of chromosome 1D, exhibiting complete resistance to three Z. tritici isolates, WAI332, WAI251, and WAI161, at the seedling stage. A genetic linkage map, based on an F2:3 population of 'Lorikeet' and 'Summit,' found the Stb19 gene at a 9.3 cM region on 1DS, closely linked with two Kompetitive Allele-Specific PCR markers, snp_4909967 and snp_1218021. Further, the two markers were tested and validated in another F2:3 population and 266 different wheat accessions, which gave over 95% accuracy of resistance/susceptibility prediction. Combined with the physical location of the identified SNPs and the previous evidence of gene order on chromosome 1DS (centromere-Sr45-Sr33-Lr21-telomere), Stb19 is proposed to be located between Sr33 and Lr21. Thus, the newly discovered Stb19 along with the KASP markers represents an increase in genetic resources available for wheat breeding resistance to Z. tritici.
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Affiliation(s)
- Nannan Yang
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Megan C McDonald
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia.
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