Summary: We present genome‐wide gene expression patterns as a time series through the infection cycle of the fungal pine needle blight pathogen, D othistroma septosporum , as it invades its gymnosperm host, P inus radiata . We determined the molecular changes at three stages of the disease cycle: epiphytic/biotrophic (early), initial necrosis (mid) and mature sporulating lesion (late). Over 1.7 billion combined plant and fungal reads were sequenced to obtain 3.2 million fungal‐specific reads, which comprised as little as 0.1% of the sample reads early in infection. This enriched dataset shows that the initial biotrophic stage is characterized by the up‐regulation of genes encoding fungal cell wall‐modifying enzymes and signalling proteins. Later necrotrophic stages show the up‐regulation of genes for secondary metabolism, putative effectors, oxidoreductases, transporters and starch degradation. This in‐depth through‐time transcriptomic study provides our first snapshot of the gene expression dynamics that characterize infection by this fungal pathogen in its gymnosperm host.

Pathogen incursions are a major impediment for global forest health. How pathogens and forest trees coexist over time, without pathogens simply killing their long-lived hosts, is a critical but unanswered question. The Dothistroma Needle Blight pathogen Dothistroma septosporum was introduced into New Zealand in the 1960s and remains a low-diversity, asexual population, providing a unique opportunity to analyze the evolution of a forest pathogen. Isolates of D. septosporum collected from commercial pine forests over 50 years were compared at whole-genome and phenotype levels. Limited genome diversity and increased diversification among recent isolates support the premise of a single introduction event. Isolates from the 1960s show significantly elevated virulence against Pinus radiata seedlings and produce higher levels of the virulence factor dothistromin compared to isolates collected in the 1990s and 2000s. However, later isolates have no increased tolerance to copper, used in fungicide treatments of infested forests and traditionally assumed to be a strong selection pressure. The isolated New Zealand population of this forest pathogen therefore appears to have become less virulent over time, likely in part to maintain the viability of its long-lived host. This finding has broad implications for forest health and highlights the benefits of long-term pathogen surveys.

Spongospora subterranea f. sp. subterranea (Sss) is a soilborne potato pathogen responsible for causing powdery scab on tubers and galls on roots, reducing root water uptake through colonizing root hairs, and vectoring of Potato mop-top virus (PMTV). However, effects of Sss on overall plant susceptibilities against subsequent infections of potato pathogens above ground have not been previously reported. This study aimed to investigate the effects of Sss on root and tuber disease expression, yield, and susceptibilities to subsequent late blight and white mold infections across six potato varieties. Sss-infected Silverton plants had 28.3% less total tuber yield and 29% fewer tubers compared to noninfected Silverton plants. We did not find a correlation across the varieties between root colonization and root gall formation. Sss-infected Silverton plants were more susceptible to hemibiotrophic late blight and less susceptible to necrotrophic white mold. Sss infection also increased susceptibilities of Goldrush and Atlantic plants to white mold. We also evaluated prevalence of asymptomatic Sss infections across the six varieties. Between 50 and 92% of the asymptomatic tubers tested positive for Sss DNA, depending on the variety. Further research is required to understand the possibility and extent of these asymptomatic infections to the spread of Sss in the field. These findings highlight the complexity of Sss-host interactions and give precedence that the lack of disease expression does not necessarily indicate resistance of a variety to Sss.

Powdery mildew disease, caused by Blumeria graminis f. sp. hordei (Bgh), which belongs to the order Erysiphales, is a major crop disease. The general control nondepressible-2 (GCN2) gene of barley was previously found to be overexpressed during the powdery mildew resistance response. Recently, Arabidopsis thaliana GCN2 (AtGCN2) was shown to be involved in disease resistance against biotrophic and necrotrophic pathogens. In order to understand the function of Hordeum vulgare GCN2 (HvGCN2) in the barley powdery mildew resistance response, this gene was silenced by barley stripe mosaic virus (BSMV), mediated by virus-induced gene silencing (VIGS). This is the first study showing the potential importance of HvGCN2 in powdery mildew disease of barley. Based on our observations, when HvGCN2 was silenced on average by 53.5%, Bgh development was increased by 18.7 to 32.1%, which was determined by primary, secondary and longest hyphae measurements. The number of germinated spores also increased 2.8-fold in HvGCN2 silenced plants compared to control plants (BSMV:00). On the other hand, under the resistant condition, no difference was observed in HvGCN2- silenced plants compared to non-silenced lines although the gene was found to be overexpressed in incompatible interaction.