Background In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. Results A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr’s adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr’s effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb ‘Starship’ transposon (dubbed ‘Horizon’) with a clearly defined target site and target site duplications. ‘Horizon’ was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative ‘Starship’ (dubbed ‘Icarus’) in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and ‘Icarus’ were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as ‘one-compartment’ based on calculated gene distances and evolutionary rates. Conclusions These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst) is an important wheat disease worldwide. In this study, the Pst population in Canada representing a time period from 1984 to 2017, was analysed for virulence diversity and geographical distribution. Virulence of 140 Pst isolates was evaluated on 17 near-isogenic wheat lines in the Avocet background each containing a single resistance gene along with an 18th line ‘Tyee’. Seedlings were inoculated with a urediniospore/talc mixture and infection types (ITs) were evaluated on a scale of 0 to 9. The results showed that Pst in Canada remains avirulent on wheat containing Yr5, and Yr15, and has very low frequency of virulence on YrTye, but has had high frequencies of virulence on Yr6, Yr7, Yr8, Yr9, Yr17, Yr43, Yr44, YrTr1, and YrExp2. Pst virulence spiked on Yr7, Yr8, and Yr9 for the first time in 2000, and Yr10 and Yr27 in 2010. Overall, the dominant races in Canada were very similar to those reported in the USA (PSTv-37, PSTv-41, and PSTv-52), which indicates long-distance migration of Pst from the USA to Canada. Analysis of diversity between Canadian isolates and races from the USA since 2010 showed that the Pst population in western Canada is similar to that in western states of the USA, and the population in eastern Canada is similar to eastern and/or central regions of the USA, supporting the hypothesis that specific Pst populations in North America travel through different wind trajectories

Parastagonospora nodorum is a fungal pathogen that causes septoria nodorum blotch in wheat. It produces several necrotrophic effectors; three have been cloned, SnToxA, SnTox1, and SnTox3. In this study, P. nodorum and its sister species Parastagonospora avenaria tritici (Pat1) were isolated from wheat node and grain samples collected from distanced sites in western Canada during 2018. The presence of effector genes and associated haplotypes were determined by PCR and sequence analysis. An ITS-RFLP test was developed to distinguish between leaf spotting pathogens including: P. nodorum, Pat1, Pyrenophora tritici-repentis and Bipolaris sorokiniana. P. nodorum was mainly recovered from wheat nodes and to a lesser extent from the grains, while Pat1 was exclusively isolated from grain samples. The effector genes were present in almost all P. nodorum isolates, with the ToxA haplotype 5 (H5) being most prevalent, while a novel ToxA haplotype (H21) is reported for the first time. In Pat1, combinations of SnTox1 and SnTox3 genes were present. A ToxA haplotype network was constructed to assess the evolutionary relationship among globally found haplotypes to date. Finally, cultivars representing wheat development in Canada for the last century were tested for sensitivity to Sn-effectors and to the presence of Tsn1, the ToxA-sensitivity gene. Of tested cultivars, 32.9% and 56.9% were sensitive to SnTox1 and SnTox3, respectively, and Tsn1 was present in 59% of the cultivars. In conclusion, P. nodorum and Pat1 were prevalent wheat pathogens in Canada with a potential specific tissue colonization capacity, while producing necrotrophic effectors to which wheat is sensitive.

Isolates of Microdochium nivale suspected of resistance to iprodione [3‐(3,5‐Dichlorophenyl)‐N‐isopropyl‐2,4‐dioxoimidazolidine‐1‐carboxamide] were collected from a golf course in Victoria, British Columbia (BC), Canada, in Fall 2015. The 9 BC isolates and 12 other reference isolates from around the world were tested with four concentrations of iprodione: 0, 1, 10, and 100 μg mL−1. The BC isolates showed a half maximal effective concentration (EC50) range of 14.2 to 40.8 μg mL−1 with a mean of 24.2 μg mL−1, while the non‐BC isolates showed an EC50 range of 1.2 to 4.3 μg mL−1 with a mean of 1.9 μg mL−1. The yielded resistance factor (EC50 resistant/EC50 sensitive) of 12.7 implies that these BC isolates have been selected for reduced sensitivity to iprodione. This level of resistance may be responsible for the reduced efficacy, particularly the observed reduced interval of control, but further research is needed to assess this. A test of >100 isolates of M. nivale from a worldwide collection using a discriminatory concentration of 10 μg mL−1 of iprodione showed four isolates with similar levels of reduced sensitivity, but these were the only isolates from their respective populations.

The fungus Pyrenophora tritici-repentis (Ptr) causes tan spot, a destructive foliar disease of wheat worldwide. The pathogen produces several necrotrophic effectors, which induce necrosis or chlorosis on susceptible wheat lines. Multiple races of Ptr have been identified, based on their ability to produce one or more of these effectors. Ptr has a wide host range of cereal and non-cereal grasses, but is known to cause damage only on wheat. Previously, we showed that Ptr can interact specifically with cultivated barley (Hordeum vulgare ssp. vulgare), and that the necrotrophic effector Ptr ToxB induces mild chlorosis in a highly selective manner when infiltrated into certain barley genotypes. In the present study, a barley doubled-haploid (DH) population was evaluated for reaction to Ptr race 5, a Ptr ToxB-producer. Then a comprehensive genetic map composed of 381 single nucleotide polymorphism (SNP) markers was used to map the locus conditioning this chlorosis. The F1 seedlings, and 92 DH lines derived from a cross between the resistant Japanese malting barley cultivar Haruna Nijo and the susceptible wild barley (H. vulgare ssp. spontaneum) OUH602 were inoculated with a conidial suspension of Ptr race 5 isolate at the two-leaf stage. The seedlings were monitored daily for symptoms and assessed for chlorosis development on the second leaf, 6 days after inoculation. All tested F1 seedlings exhibited chlorosis symptoms similar to the susceptible parent, and the DH lines segregated 1:1 for susceptible:resistant phenotypes, indicating the involvement of a single locus. Marker-trait linkage analysis based on interval mapping identified a single locus on the distal region of the short arm of chromosome 2H. We designate this locus Susceptibility to P. tritici-repentis1 (Spr1). The region encompassing this locus has 99 high confidence gene models, including membrane receptor-like kinases (RLKs), intracellular nucleotide-binding, leucine-rich repeat receptors (NLRs), and ankyrin-repeat proteins (ANKs). This shows the involvement of a dominant locus conferring susceptibility to Ptr in barley. Further work using high-resolution mapping and transgenic complementation will be required to identify the underlying gene.