Highly Repetitive Genome of Coniella granati (syn. Pilidiella granati), the Causal Agent of Pomegranate Fruit Rot, Encodes a Minimalistic Proteome with a Streamlined Arsenal of Effector Proteins.

This study describes the first genome sequence and analysis of Coniella granati, a fungal pathogen with a broad host range, which is responsible for postharvest crown rot, shoot blight, and canker diseases in pomegranates. C. granati is a geographically widespread pathogen which has been reported across Europe, Asia, the Americas, and Africa. Our analysis revealed a 46.8 Mb genome with features characteristic of hemibiotrophic fungi. Approximately one third of its genome was compartmentalised within 'AT-rich' regions exhibiting a low GC content (30 to 45%). These regions primarily comprised transposable elements that are repeated at a high frequency and interspersed throughout the genome. Transcriptome-supported gene annotation of the C. granati genome revealed a streamlined proteome, mirroring similar observations in other pathogens with a latent phase. The genome encoded a relatively compact set of 9568 protein-coding genes with a remarkable 95% having assigned functional annotations. Despite this streamlined nature, a set of 40 cysteine-rich candidate secreted effector-like proteins (CSEPs) was predicted as well as a gene cluster involved in the synthesis of a pomegranate-associated toxin. These potential virulence factors were predominantly located near repeat-rich and AT-rich regions, suggesting that the pathogen evades host defences through Repeat-Induced Point mutation (RIP)-mediated pseudogenisation. Furthermore, 23 of these CSEPs exhibited homology to known effector and pathogenicity genes found in other hemibiotrophic pathogens. The study establishes a foundational resource for the study of the genetic makeup of C. granati, paving the way for future research on its pathogenicity mechanisms and the development of targeted control strategies to safeguard pomegranate production.

Pan-genome survey of Septoria pistaciarum, causal agent of Septoria leaf spot of pistachios, across three Aegean sub-regions of Greece.

Septoria pistaciarum, a causal agent of Septoria leaf spot disease of pistachio, is a fungal pathogen that causes substantial losses in the cultivation, worldwide. This study describes the first pan-genome-based survey of this phytopathogen-comprising a total of 27 isolates, with 9 isolates each from 3 regional units of Greece (Pieria, Larissa and Fthiotida). The reference isolate (SPF8) assembled into a total of 43.1 Mb, with 38.6% contained within AT-rich regions of approximately 37.5% G:C. The genomes of the 27 isolates exhibited on average 42% gene-coding and 20% repetitive regions. The genomes of isolates from the southern Fthiotida region appeared to more diverged from each other than the other regions based on SNP-derived trees, and also contained isolates similar to both the Pieria and Larissa regions. In contrast, isolates of the Pieria and Larissa were less diverse and distinct from one another. Asexual reproduction appeared to be typical, with no MAT1-2 locus detected in any isolate. Genome-based prediction of infection mode indicated hemibiotrophic and saprotrophic adaptations, consistent with its long latent phase. Gene prediction and orthology clustering generated a pan-genome-wide gene set of 21,174 loci. A total of 59 ortholog groups were predicted to contain candidate effector proteins, with 36 (61%) of these either having homologs to known effectors from other species or could be assigned predicted functions from matches to conserved domains. Overall, effector prediction suggests that S. pistaciarum employs a combination of defensive effectors with roles in suppression of host defenses, and offensive effectors with a range of cytotoxic activities. Some effector-like ortholog groups presented as divergent versions of the same protein, suggesting region-specific adaptations may have occurred. These findings provide insights and future research directions in uncovering the pathogenesis and population dynamics of S. pistaciarum toward the efficient management of Septoria leaf spot of pistachio.

Tree host-pathogen interactions as influenced by drought timing: linking physiological performance, biochemical defence and disease severity.

There is increasing concern about tree mortality around the world due to climatic extremes and associated shifts in pest and pathogen dynamics. Yet, empirical studies addressing the interactive effect of biotic and abiotic stress on plants are very rare. Therefore, in this study, we examined the interaction between drought stress and a canker pathogen, Quambalaria coyrecup, on the eucalypt - Corymbia calophylla (marri), which is experiencing increasing drought stress. We hypothesized that drought stress would increase marri's susceptibility to canker disease, and cankers would have the largest negative effect on plants that are already drought stressed before pathogen inoculation. To test the hypotheses, in a glasshouse, marri saplings were exposed to drought either before or after pathogen inoculation, or were well-watered or droughted throughout the experiment either with or without inoculation. Canker development was greater in well-watered saplings than in droughted saplings, with the fastest development occurring in well-watered saplings that had experienced drought stress before inoculation. Irrespective of water treatments, marri saplings employed phenol-based localized biochemical defence against the pathogen. Drought reduced photosynthesis and growth, however, a negative effect of canker disease on saplings' physiological performance was only observed in well-watered saplings. In well-watered saplings, canker-induced loss of sapwood function contributed to reduced whole-plant hydraulic conductance, photosynthesis and growth. The results provide evidence that timing of drought stress influences host physiology, and host condition influences canker disease susceptibility through differences in induced biochemical defence mechanisms. The observations highlight the importance of explicitly incorporating abiotic and biotic stress, as well as their interactions, in future studies of tree mortality in drought-prone regions worldwide.

Immediate and potential long-term effects of consecutive heat waves on the photosynthetic performance and water balance in Douglas-fir.

The frequency and intensity of climatic extremes, such as heat waves, are predicted to increase globally, with severe implications for terrestrial carbon and water cycling. Temperatures may rise above critical thresholds that allow trees to function optimally, with unknown long-term consequences for forest ecosystems. In this context, we investigated how photosynthetic traits and the water balance in Douglas-fir are affected by exposure to three heat waves with temperatures about 12°C above ambient. Photosynthetic carboxylation efficiency (Vcmax) was mostly unaffected, but electron transport (Jmax) and photosynthetic rates under saturating light (Asat) were strongly influenced by the heat waves, with lagging limitations on photosynthesis still being observed six weeks after the last heat wave. We also observed lingering heat-induced inhibitions on transpiration, minimum stomatal conductance, and night-time stomatal conductance (gs-night). Results from the stomatal models used to calculate minimum stomatal conductance were similar to gs-night and indicated changes in leaf morphology, e.g. stomatal occlusions and alterations in epicuticular wax. Our results show Douglas-fir's ability to restrict water loss following heat stress, but at the price of reduced photosynthetic performance. Such limitations indicate potential long-term restrictions that heat waves can impose on tree development and functioning under extreme climatic conditions.