Evolutionary Genomics of the Wheat Stripe Rust Pathogen, Puccinia striiformis f. sp. tritici

Abstract

Wheat is a cornerstone crop for global food security, providing approximately 20% of the world's calories and protein. However, wheat production is increasingly threatened by both biotic and abiotic stresses. Among the most significant biotic threats is stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), a biotrophic basidiomycete fungus. Over the past two decades, PST has expanded its geographic range, entering regions previously unaffected by stripe rust. This expansion is correlated with increased genetic diversity in PST populations, which were formerly dominated by a single clonal lineage. In this thesis, I conducted a comprehensive phylogenomic analysis of PST using whole-genome sequencing (WGS) data from 122 isolates collected from diverse wheat-growing regions. Six isolates from Australia were sequenced in this study, while the remaining data were sourced from previously published studies. By integrating global and Australian data, I aimed to explore the population dynamics and evolutionary patterns of PST. A key contribution of my research is the assembly of full-length mitochondrial genomes for three major PST lineages using long PacBio reads. These genomes served as references for extracting mitochondrial sequences from Illumina data, enabling detailed analyses of mitochondrial variation. Although coding regions were highly conserved, three variable sites were identified in the nad5 and nad6 genes, defining four mitochondrial haplotypes: Pst-mtH-S0, Pst-mtH-S1, Pst-mtH-S7/8, and Ps-mtH-fs. These haplotypes were associated with major PST lineages and were used to identify apparent heteroplasmy in 29 isolates primarily from Canada, suggestive of somatic hybridisation. In addition to mitochondrial analysis, I conducted whole-genome variation analysis across the 122 isolates. Phylogenetic and population genetic analyses revealed nine major clades corresponding to established PST lineages, including PstS0, PstS1, PstS7/8, PstS10, PstS13, and a new lineage that I designated PsS-fs (forma specialis). Some subpopulations, such as the Canadian-specific PstS1-CA1 and South African-origin PstS1-SA, were novel or difficult to associate with known lineages. My genome-wide analysis also challenged previous classifications that split PstS7/8 into distinct lineages (PstS7 and PstS8). Instead, my data indicate they represent variants of the same lineage, with evidence of a close relationship between European PstS7/8 and US isolates (PST-127 and PST-130) from 2008, suggesting a broader geographic distribution and earlier emergence of this lineage than recognised previously. I further explored genome heterozygosity and divergence between subpopulations, finding that PstS-AF/IN and PstS7/8 are among the most genetically diverse and least heterozygous, indicating recent sexual origins. The PstS7/8 subpopulation, first identified in Europe in 2011, likely originated from the Himalayan region. However, the highly homozygous PstS-AF/IN subpopulation from northeastern Africa is highly divergent from PstS7/8 and unlikely to have come from the Himalayas, suggesting possible sexual reproduction in Africa. Additionally, this thesis reports relatively low genetic divergence between wheat and non-wheat isolates (PsS-fs), which is unusual for pathogens that specialise to different hosts. Admixture analysis suggests that the low divergence may result from asexual genetic exchange between PST and PsS-fs, explaining their overlapping host boundaries. Finally, admixture analyses revealed extensive genetic exchange in global PST populations, particularly in the Canadian PstS1-CA1 subpopulation, further supporting the hypothesis that this lineage likely evolved from somatic hybridisation between PstS1 and PstS7/8. In conclusion, this thesis provides a comprehensive analysis of global PST subpopulations, offering valuable insights into the evolutionary dynamics and population structures of this critical wheat pathogen. Show more