Adaptation to the Host Environment by Plant-Pathogenic Fungi

Positive selection and functional diversification of transcription factor Cmr1 homologs in Alternaria

Transcription factor Cmr1 (Colletotrichum melanin regulation 1) and its homologs in several plant fungal pathogens are the regulators of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis pathway and have evolved functional diversification in morphology and pathogenicity. The fungal genus Alternaria comprises the group of "black fungi" that are rich in DHN-melanin in the primary cell wall and septa of the conidia. Some Alternaria species cause many economically important plant diseases worldwide. However, the evolution and function of Cmr1 homologs in Alternaria remain poorly understood. Here, we identified a total of forty-two Cmr1 homologs from forty-two Alternaria spp. and all contained one additional diverse fungal specific transcription factor motif. Phylogenetic analysis indicated the division of these homologs into five major clades and three branches. Dated phylogeny showed the A and D clades diverged latest and earliest, respectively. Molecular evolutionary analyses revealed that three amino acid sites of Cmr1 homologs in Alternaria were the targets of positive selection. Asmr1, the homolog of Cmr1 in the potato early blight pathogen, Alternaria solani was amplified and displayed the sequence conservation at the amino acid level in different A. solani isolates. Asmr1 was further confirmed to have the transcriptional activation activity and was upregulated during the early stage of potato infection. Deletion of asmr1 led to the decreased melanin content and pathogenicity, deformed conidial morphology, and responses to cell wall and fungicide stresses in A. solani. These results suggest positive selection and functional divergence have played a role in the evolution of Cmr1 homologs in Alternaria. KEY POINTS: • Cmr1 homologs were under positive selection in Alternaria species • Asmr1 is a functional transcription factor, involved in spore development, melanin biosynthesis, pathogenicity, and responses to cell wall and fungicide stresses in A. solani • Cmr1 might be used as a potential taxonomic marker of the genus Alternaria.

Drought: A context-dependent damper and aggravator of plant diseases

Drought dynamically influences the interactions between plants and pathogens, thereby affecting disease outbreaks. Understanding the intricate mechanistic aspects of the multiscale interactions among plants, pathogens, and the environment-known as the disease triangle-is paramount for enhancing the climate resilience of crop plants. In this review, we systematically compile and comprehensively analyse current knowledge on the influence of drought on the severity of plant diseases. We emphasise that studying these stresses in isolation is not sufficient to predict how plants respond to combined stress from both drought and pathogens. The impact of drought and pathogens on plants is complex and multifaceted, encompassing the activation of antagonistic signalling cascades in response to stress factors. The nature, intensity, and temporality of drought and pathogen stress occurrence significantly influence the outcome of diseases. We delineate the drought-sensitive nodes of plant immunity and highlight the emerging points of crosstalk between drought and defence signalling under combined stress. The limited mechanistic understanding of these interactions is acknowledged as a key research gap in this area. The information synthesised herein will be crucial for crafting strategies for the accurate prediction and mitigation of future crop disease risks, particularly in the context of a changing climate.

Fungal Cell Wall-Associated Effectors: Sensing, Integration, Suppression, and Protection

The cell wall (CW) of plant-interacting fungi, as the direct interface with host plants, plays a crucial role in fungal development. A number of secreted proteins are directly associated with the fungal CW, either through covalent or non-covalent interactions, and serve a range of important functions. In the context of plant-fungal interactions many are important for fungal development in the host environment and may therefore be considered fungal CW-associated effectors (CWAEs). Key CWAE functions include integrating chemical/physical signals to direct hyphal growth, interfering with plant immunity, and providing protection against plant defenses. In recent years, a diverse range of mechanisms have been reported that underpin their roles, with some CWAEs harboring conserved motifs or functional domains, while others are reported to have novel features. As such, the current understanding regarding fungal CWAEs is systematically presented here from the perspective of their biological functions in plant-fungal interactions. An overview of the fungal CW architecture and the mechanisms by which proteins are secreted, modified, and incorporated into the CW is first presented to provide context for their biological roles. Some CWAE functions are reported across a broad range of pathosystems or symbiotic/mutualistic associations. Prominent are the chitin interacting-effectors that facilitate fungal CW modification, protection, or suppression of host immune responses. However, several alternative functions are now reported and are presented and discussed. CWAEs can play diverse roles, some possibly unique to fungal lineages and others conserved across a broad range of plant-interacting fungi. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations

Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.

Activation of Ustilaginoidin Biosynthesis Gene uvpks1 in Villosiclava virens Albino Strain LN02 Influences Development, Stress Responses, and Inhibition of Rice Seed Germination

Villosiclava virens (anamorph: Ustilaginoidea virens) is the pathogen of rice false smut (RFS), which is a destructive rice fungal disease. The albino strain LN02 is a natural white-phenotype mutant of V. virens due to its incapability to produce toxic ustilaginoidins. In this study, three strains including the normal strain P1, albino strain LN02, and complemented strain uvpks1C-1 of the LN02 strain were employed to investigate the activation of the ustilaginoidin biosynthesis gene uvpks1 in the albino strain LN02 to influence sporulation, conidia germination, pigment production, stress responses, and the inhibition of rice seed germination. The activation of the ustilaginoidin biosynthesis gene uvpks1 increased fungal tolerances to NaCl-induced osmotic stress, Congo-red-induced cell wall stress, SDS-induced cell membrane stress, and H2O2-induced oxidative stress. The activation of uvpks1 also increased sporulation, conidia germination, pigment production, and the inhibition of rice seed germination. In addition, the activation of uvpks1 was able to increase the mycelial growth of the V. virens albino strain LN02 at 23 °C and a pH from 5.5 to 7.5. The findings help in understanding the effects of the activation of uvpks1 in albino strain LN02 on development, pigment production, stress responses, and the inhibition of rice seed germination by controlling ustilaginoidin biosynthesis.

Cuscuta campestris fine-tunes gene expression during haustoriogenesis as an adaptation to different hosts

The Cuscuta genus comprises obligate parasitic plants that have an unusually wide host range. Whether Cuscuta uses different infection strategies for different hosts or whether the infection strategy is mechanistically and enzymatically conserved remains unknown. To address this, we investigated molecular events during the interaction between field dodder (Cuscuta campestris) and two host species of the Solanum genus that are known to react differently to parasitic infection. We found that host gene induction, particularly of cell wall fortifying genes, coincided with a differential induction of genes for cell wall degradation in the parasite in the cultivated tomato (Solanum lycopersicum) but not in a wild relative (Solanum pennellii). This indicates that the parasite can adjust its gene expression in response to its host. This idea was supported by the increased expression of C. campestris genes encoding an endo-β-1,4-mannanase in response to exposure of the parasite to purified mono- and polysaccharides in a host-independent infection system. Our results suggest multiple key roles of the host cell wall in determining the outcome of an infection attempt.

Gene Family Expansion during the Adaptation of Colletotrichum gloeosporioides to Woody Plants

Gene gains/losses during evolution are critical for the adaptation of organisms to new environments or hosts. However, it remains unknown whether gene family expansions facilitated the adaptation of phytopathogenic fungi to woody plants. In this study, we compared the newly sequenced genome of the Colletotrichum gloeosporioides strain CFCC80308 with the genomes of two other C. gloeosporioides strains, Cg-14 and Lc-1, isolated from Persea americana and Liriodendron leaves, respectively. The genes in the expanded families, which were associated with plant surface signal recognition, encoded various proteins, including glycosyde hydrolases (GHs) and cytochrome P450. Interestingly, there was a substantial increase in the number of GH family genes in CFCC80308. Specifically, there were 368 enriched genes in the GH families (e.g., GH1, GH3, GH10, GH12, GH15, GH16, GH17, GH18, GH25, GH32, GH53, GH61, GH76, and GH81); the expression levels of these genes were highly up-regulated during the infection of poplar trees. Additionally, the GH17 family was larger in CFCC80308 than in C. gloeosporioides strains Cg-14 and Lc-1. Furthermore, the expansion of the MP65-encoding gene family during the adaptation of Colletotrichum species to woody plants was consistent with the importance of gene gains/losses for the adaptation of organisms to their environments. This study has clarified how C. gloeosporioides adapted to woody plants during evolution.

Polygenic pathogen networks influence transcriptional plasticity in the Arabidopsis-Botrytis pathosystem

Bidirectional flow of information shapes the outcome of the host-pathogen interactions and depends on the genetics of each organism. Recent work has begun to use co-transcriptomic studies to shed light on this bidirectional flow, but it is unclear how plastic the co-transcriptome is in response to genetic variation in both the host and pathogen. To study co-transcriptome plasticity, we conducted transcriptomics using natural genetic variation in the pathogen, Botrytis cinerea, and large-effect genetic variation abolishing defense signaling pathways within the host, Arabidopsis thaliana. We show that genetic variation in the pathogen has a greater influence on the co-transcriptome than mutations that abolish defense signaling pathways in the host. Genome-wide association mapping using the pathogens' genetic variation and both organisms' transcriptomes allowed an assessment of how the pathogen modulates plasticity in response to the host. This showed that the differences in both organism's responses were linked to trans-expression quantitative trait loci (eQTL) hotspots within the pathogen's genome. These hotspots control gene sets in either the host or pathogen and show differential allele sensitivity to the host's genetic variation rather than qualitative host specificity. Interestingly, nearly all the trans-eQTL hotspots were unique to the host or pathogen transcriptomes. In this system of differential plasticity, the pathogen mediates the shift in the co-transcriptome more than the host.

Verticillium dahliae Vta3 promotes ELV1 virulence factor gene expression in xylem sap, but tames Mtf1-mediated late stages of fungus-plant interactions and microsclerotia formation

Verticillium transcription activator of adhesion 3 (Vta3) is required for plant root colonization and pathogenicity of the soil-borne vascular fungus Verticillium dahliae. RNA sequencing identified Vta3-dependent genetic networks required for growth in tomato xylem sap. Vta3 affects the expression of more than 1,000 transcripts, including candidates with predicted functions in virulence and morphogenesis such as Egh16-like virulence factor 1 (Elv1) and Master transcription factor 1 (Mtf1). The genes encoding Elv1 and Mtf1 were deleted and their functions in V. dahliae growth and virulence on tomato (Solanum lycopersicum) plants were investigated using genetics, plant infection experiments, gene expression studies and phytohormone analyses. Vta3 contributes to virulence by promoting ELV1 expression, which is dispensable for vegetative growth and conidiation. Vta3 decreases disease symptoms mediated by Mtf1 in advanced stages of tomato plant colonization, while Mtf1 induces the expression of fungal effector genes and tomato pathogenesis-related protein genes. The levels of pipecolic and salicylic acids functioning in tomato defense signaling against (hemi-) biotrophic pathogens depend on the presence of MTF1, which promotes the formation of resting structures at the end of the infection cycle. In summary, the presence of VTA3 alters gene expression of virulence factors and tames the Mtf1 genetic subnetwork for late stages of plant disease progression and subsequent survival of the fungus in the soil.

Dual impact of ambient humidity on the virulence of Magnaporthe oryzae and basal resistance in rice

Humidity is a critical environmental factor affecting the epidemic of plant diseases. However, it is still unclear how ambient humidity affects the occurrence of diseases in plants. In this study, we show that high ambient humidity enhanced blast development in rice plants under laboratory conditions. Furthermore, we found that high ambient humidity enhanced the virulence of Magnaporthe oryzae by promoting conidial germination and appressorium formation. In addition, the results of RNA-sequencing analysis and the ethylene content assessment revealed that high ambient humidity suppressed the accumulation of ethylene and the activation of ethylene signaling pathway induced by M. oryzae in rice. Knock out of ethylene signaling genes OsEIL1 and OsEIN2 or exogenous application of 1-methylcyclopropene (ethylene inhibitor) and ethephon (ethylene analogues) eliminated the difference of blast resistance between the 70% and 90% relative humidity conditions, suggesting that the activation of ethylene signaling contributes to humidity-modulated basal resistance against M. oryzae in rice. In conclusion, our results demonstrated that high ambient humidity enhances the virulence of M. oryzae and compromises basal resistance by reducing the activation of ethylene biosynthesis and signaling in rice. Results from this study provide cues for novel strategies to control rice blast under global environmental changes.

Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress

Poaceae plants can locally accumulate iron to suppress pathogen infection. It remains unknown how pathogens overcome host-derived iron stress during their successful infections. Here, we report that Fusarium graminearum (Fg), a destructive fungal pathogen of cereal crops, is challenged by host-derived high-iron stress. Fg infection induces host alkalinization, and the pH-dependent transcription factor FgPacC undergoes a proteolytic cleavage into the functional isoform named FgPacC30 under alkaline host environment. Subsequently FgPacC30 binds to a GCCAR(R = A/G)G element at the promoters of the genes involved in iron uptake and inhibits their expression, leading to adaption of Fg to high-iron stress. Mechanistically, FgPacC30 binds to FgGcn5 protein, a catalytic subunit of Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, leading to deregulation of histone acetylation at H3K18 and H2BK11, and repression of iron uptake genes. Moreover, we identified a protein kinase FgHal4, which is highly induced by extracellular high-iron stress and protects FgPacC30 against 26S proteasome-dependent degradation by promoting FgPacC30 phosphorylation at Ser2. Collectively, this study uncovers a novel inhibitory mechanism of the SAGA complex by a transcription factor that enables a fungal pathogen to adapt to dynamic microenvironments during infection.

Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence

Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, yet relatively few virulence-specific regulators are characterised in detail and their evolutionary trajectories are not well understood. Hence, this study compared the full range of TFs across taxonomically-diverse fungal proteomes and classified their lineages through an orthology analysis. The primary aims were to characterise differences in the range and profile of TF lineages broadly linked to plant-host association or pathogenic lifestyles, and to better characterise the evolutionary origin and trajectory of experimentally-validated virulence regulators. We observed significantly fewer TFs among obligate, host-associated pathogens, largely attributed to contractions in several Zn2Cys6 TF-orthogroup lineages. We also present novel insight into the key virulence-regulating TFs Ste12, Pf2 and EBR1, providing evidence for their ancestral origins, expansion and/or loss. Ultimately, the analysis presented here provides both primary evidence for TF evolution in fungal phytopathogenicity, as well as a practical phylogenetic resource to guide further detailed investigation on the regulation of virulence within key pathogen lineages.

Convergence Analysis of Rust Fungi and Anther Smuts Reveals Their Common Molecular Adaptation to a Phytoparasitic Lifestyle

Convergent evolution between distantly related taxa often mirrors adaptation to similar environments. Rust fungi and anther smuts, which belong to different classes in Pucciniomycotina, have independently evolved a phytoparasitic lifestyle, representing an example of convergent evolution in the fungal kingdom. To investigate their adaptations and the genetic bases underlying their phytoparasitic lifestyles, we performed genome-wide convergence analysis of amino acid substitutions, evolutionary rates, and gene gains and losses. Convergent substitutions were detected in ATPeV0D and RP-S27Ae, two genes important for the generation of turgor pressure and ribosomal biosynthesis, respectively. A total of 51 positively selected genes were identified, including eight genes associated with translation and three genes related to the secretion pathway. In addition, rust fungi and anther smuts contained more proteins associated with oligopeptide transporters and vacuolar proteases than did other fungi. For rust fungi and anther smuts, these forms of convergence suggest four adaptive mechanisms for a phytoparasitic lifestyle: 1) reducing the metabolic demand for hyphal growth and penetration at the pre-penetration stage, 2) maintaining the efficiency of protein synthesis during colonization, 3) ensuring the normal secretion of rapidly evolving secreted proteins, and 4) improving the capacity for oligopeptide metabolism. Our results are the first to shed light on the genetic convergence mechanisms and molecular adaptation underlying phytoparasitic lifestyles in fungi.

Marchantia polymorpha model reveals conserved infection mechanisms in the vascular wilt fungal pathogen Fusarium oxysporum

Root-infecting vascular fungi cause wilt diseases and provoke devastating losses in hundreds of crops. It is currently unknown how these pathogens evolved and whether they can also infect nonvascular plants, which diverged from vascular plants over 450 million years ago. We established a pathosystem between the nonvascular plant Marchantia polymorpha (Mp) and the root-infecting vascular wilt fungus Fusarium oxysporum (Fo). On angiosperms, Fo exhibits exquisite adaptation to the plant xylem niche as well as host-specific pathogenicity, both of which are conferred by effectors encoded on lineage-specific chromosomes. Fo isolates displaying contrasting lifestyles on angiosperms - pathogenic vs endophytic - are able to infect Mp and cause tissue maceration and host cell killing. Using isogenic fungal mutants we define a set of conserved fungal pathogenicity factors, including mitogen activated protein kinases, transcriptional regulators and cell wall remodelling enzymes, that are required for infection of both vascular and nonvascular plants. Markedly, two host-specific effectors and a morphogenetic regulator, which contribute to vascular colonisation and virulence on tomato plants are dispensable on Mp. Collectively, these findings suggest that vascular wilt fungi employ conserved infection strategies on nonvascular and vascular plant lineages but also have specific mechanisms to access the vascular niche of angiosperms.

Synthesis and Antifungal Activity of Novel Tetrahydrogeranyl Quaternary Ammonium Salts

Due to the excessive use of antifungal agents, drug resistance and ecological problems are increasing. Some antifungal agents are difficult to degrade and have high toxicity and several side effects. In this study, 15 novel tetrahydrogeranyl quaternary ammonium salts (8a–8o) were synthesized from the natural compound citral. The structures of the quaternary ammonium salts were characterized by Fourier transform infrared, proton nuclear magnetic resonance, carbon-13 nuclear magnetic resonance spectroscopy, and mass spectrometry, and the antifungal activities of these compounds at a concentration of 0.25 mg/mL against 10 plant pathogenic fungi were tested. The results showed that compound 8i had the best antifungal activity, and its inhibition rates against Rhizoctonia solani, Phytophthora parasitica var. nicotianae, Sphaeropsis sapinea, Fusarium oxysporum f. sp. niveum, and Poria vaporaria reached 100%. For Fusarium verticillioides, the inhibition rate of compound 8i was 93.28%, which was higher than that of chlorothalonil. In addition, it was found that the inhibition rates of compounds with N,N-di- n-propyl group (8l, 8m) against R solani, F oxysporum f. sp. niveum, S sapinea, P parasitica var. nicotianae, F verticillioides, Colletotrichum acutatum, and Coriolus versicolor were higher than compounds with N,N-diethyl and N,N-dimethyl groups (8a, 8b, 8j, 8k). The inhibition rates of compounds with morpholine groups (8n, 8o) were generally low.

Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry (Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis

The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.

Biosynthesis, regulation, and biological significance of fumonisins in fungi: current status and prospects

Fumonisins are one of the most important mycotoxin classes due to their widespread occurrence and potential health threat to humans and animals. Currently, most of the research focuses on the control of fumonisin contamination in the food supply chain. In recent years, significant progress in biochemistry, enzymology, and genetic regulation of fumonisin biosynthesis has been achieved using molecular technology. Furthermore, new insights into the roles of fumonisins in the interaction between fungi and plant hosts have been reported. This review provides an overview of the current understanding of the biosynthesis and regulation of fumonisins. The ecological significance of fumonisins to Fusarium species that produce the toxins is discussed, and the complex regulatory networks of fumonisin synthesis is proposed.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

Contrasting transcriptional responses to Fusarium virguliforme colonization in symptomatic and asymptomatic hosts

The broad host range of Fusarium virguliforme represents a unique comparative system to identify and define differentially induced responses between an asymptomatic monocot host, maize (Zea mays), and a symptomatic eudicot host, soybean (Glycine max). Using a temporal, comparative transcriptome-based approach, we observed that early gene expression profiles of root tissue from infected maize suggest that pathogen tolerance coincides with the rapid induction of senescence dampening transcriptional regulators, including ANACs (Arabidopsis thaliana NAM/ATAF/CUC protein) and Ethylene-Responsive Factors. In contrast, the expression of senescence-associated processes in soybean was coincident with the appearance of disease symptom development, suggesting pathogen-induced senescence as a key pathway driving pathogen susceptibility in soybean. Based on the analyses described herein, we posit that root senescence is a primary contributing factor underlying colonization and disease progression in symptomatic versus asymptomatic host-fungal interactions. This process also supports the lifestyle and virulence of F. virguliforme during biotrophy to necrotrophy transitions. Further support for this hypothesis lies in comprehensive co-expression and comparative transcriptome analyses, and in total, supports the emerging concept of necrotrophy-activated senescence. We propose that F. virguliforme conditions an environment within symptomatic hosts, which favors susceptibility through transcriptomic reprogramming, and as described herein, the induction of pathways associated with senescence during the necrotrophic stage of fungal development.

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.

Vm-milR37 contributes to pathogenicity by regulating glutathione peroxidase gene VmGP in Valsa mali

MicroRNAs play important roles in various biological processes by regulating their corresponding target genes. However, the function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) are still largely unknown. In this study, a milRNA (Vm-milR37) was isolated and identified from Valsa mali, which causes the most serious disease on the trunk of apple trees in China. Based on the results of deep sequencing and quantitative reverse transcription PCR, Vm-milR37 was found to be expressed in the mycelium, while it was not expressed during the V. mali infection process. Overexpression of Vm-milR37 did not affect vegetative growth, but significantly decreased pathogenicity. Based on degradome sequencing, the target of Vm-milR37 was identified as VmGP, a glutathione peroxidase. The expression of Vm-milR37 and VmGP showed a divergent trend in V. mali-apple interaction samples and Vm-milR37 overexpression transformants. The expression of VmGP could be suppressed significantly by Vm-milR37 when coexpressed in tobacco leaves. Deletion of VmGP showed significantly reduced pathogenicity compared with the wild type. VmGP deletion mutants showed more sensitivity to hydrogen peroxide. Apple leaves inoculated with Vm-milR37 overexpression transformants and VmGP deletion mutant displayed increased accumulation of reactive oxygen species compared with the wild type. Thus, Vm-milR37 plays a critical role in pathogenicity by regulating VmGP, which contributes to the oxidative stress response during V. mali infection. These results provide important evidence to define the roles of milRNAs and their corresponding target genes in pathogenicity.

Validation of an in vitro system to trigger changes in the gene expression of effectors of Sclerotinia sclerotiorum

AIMS

Sclerotinia sclerotiorum, the causal agent of white mold, can infect several host species, including economically important crops. In this study, we propose and validate a new in vitro system able to mimic the conditions of interaction with the host and promote the induction of S. sclerotiorum effectors.

METHODS AND RESULTS

For culture media production, we selected three plant species, common bean (Phaseolus vulgaris L, cv. Requinte.), maize (Zea mays, cv. BRS1030) and beggarticks (Bidens pilosa). To validate this system as an in vitro inducer of effectors, the qRT-PCR technique was used to investigate the expression profile of some S. sclerotiorum effector genes in each growth medium at different times after inoculation.

CONCLUSION

The results obtained in this study provide a validation of a new method to study S. sclerotiorum during mimetic interaction with different hosts. Although leaf extract does not fully represent the plant environment, the presence of plant components in the culture medium seems to induce effector genes, mimicking in planta conditions. The use of MEVM is simpler than in planta growth, bypasses problems such as the amount of mycelium produced, as well as contamination of host cells during transcriptomic and proteomic analyses.

SIGNIFICANCE AND IMPACT OF THE STUDY

We have devised MEVM media as a model mimicking the interaction of S. sclerotiorum and its hosts and used it to evaluate in vitro expression of effectors normally expressed only in planta.

Genome-wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families

Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3' receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.

Phytochemical and Antioxidant Dynamics of the Soursop Fruit (Annona muricata L.) in response to Colletotrichum spp

This work evaluates the effect of the pathogens Colletotrichum siamense and C. gloeosporioides on the response of soursop fruits. The bioactive compounds (total phenols, flavonoids, anthraquinones, coumarins, steroids, terpenoids, alkaloids, and saponins) were evaluated qualitatively in soursop pulp. Positive phytochemicals and antioxidant activity (DPPH•, ABTS•+, and FRAP) were quantified at day zero, one, three, and five. Fruits treated with C. gloeosporioides showed higher disease severity (P<0.05). Early fruit response (day one) was observed with both pathogens, increased the concentration of saponins and repressed the production of quercetin 3-O-glucoside (P<0.05). Likewise, C. siamense decreased total soluble phenols and flavonoids and increased antiradical activity DPPH•. Besides, C. gloeosporioides decreased the levels of kaempferol 3-O-rutinoside and ferulic acid (P<0.05). Regarding the late response (day three), both pathogens decreased the concentration of saponins and increased flavonoids and phytosterols (P<0.05). Nevertheless, C. siamense increased the levels of total soluble phenols, p-coumaric acid, kaempferol, and antiradical activity FRAP (P<0.05). Also, C. gloeosporioides repressed the production of quercetin 3-O-glucoside at day five (P<0.05). Soursop fruits had a response to the attack of Colletotrichum during ripening at physicochemical and oxidative levels, which is associated with the production of compounds related to the development inhibition of pathogens. Even so, soursop fruits showed higher susceptibility to C. gloeosporioides and higher sensitivity to the attack of C. siamense.

Real-Time Visualization of Cellulase Activity by Microorganisms on Surface

A variety of methods to detect cellulase secretion by microorganisms has been developed over the years, none of which enables the real-time visualization of cellulase activity on a surface. This visualization is critical to study the interaction between soil-borne cellulase-secreting microorganisms and the surface of plant roots and specifically, the effect of surface features on this interaction. Here, we modified the known carboxymethyl cellulase (CMC) hydrolysis visualization method to enable the real-time tracking of cellulase activity of microorganisms on a surface. A surface was formed using pure CMC with acridine orange dye incorporated in it. The dye disassociated from the film when hydrolysis occurred, forming a halo surrounding the point of hydrolysis. This enabled real-time visualization, since the common need for post hydrolysis dyeing was negated. Using root-knot nematode (RKN) as a model organism that penetrates plant roots, we showed that it was possible to follow microorganism cellulase secretion on the surface. Furthermore, the addition of natural additives was also shown to be an option and resulted in an increased RKN response. This method will be implemented in the future, investigating different microorganisms on a root surface microstructure replica, which can open a new avenue of research in the field of plant root-microorganism interactions.

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

Background

Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome structure may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome, has emerged as a model organism to study genome evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and of sister species infecting wild grasses to address the evolution of genome composition and structure.

Results

Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, predicted effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts.

Conclusion

Despite previous reports of high genomic plasticity in Z. tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria. The compartmentalized genome allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.

Functional Ecology of Forest Disease

Global change is pressing forest pathologists to solve increasingly complex problems. We argue that understanding interactive effects between forest pathogens and global warming, globalization, and land-use changes may benefit from a functional ecology mindset. Traits can be more informative about ecological functions than species inventories and may deliver a more mechanistic description of forest disease. Myriad microbes with pathogenic potential interact with forest ecosystems at different organizational levels. Elucidation of functional traits may enable the microbial complexity to be reduced into manageable categories with predictive power. In this review, we propose guidelines that allow the research community to develop a functional forest pathology approach. We suggest new angles by which functional questions can be used to resolve burning issues on tree disease. Building up functional databases for pathogenicity is key to implementing these approaches.

Adaptive regulation of virulence genes by microRNA-like RNAs in Valsa mali

MicroRNAs play important roles in the regulation of gene expression in plants and animals. However, little information is known about the action mechanism and function of fungal microRNA-like RNAs (milRNAs). In this study, combining deep sequencing, molecular and histological assays, milRNAs and their targets in the phytopathogenic fungus Valsa mali were isolated and identified. A critical milRNA, Vm-milR16, was identified to adaptively regulate the expression of virulence genes. Fourteen isolated milRNAs showed high expression abundance. Based on the assessment of a pathogenicity function of these milRNAs, Vm-milR16 was found to be a critical milRNA in V. mali by regulating sucrose non-fermenting 1 (VmSNF1), 4,5-DOPA dioxygenase extradiol (VmDODA), and a hypothetical protein (VmHy1). During V. mali infection, Vm-milR16 is downregulated, while its targets are upregulated. Overexpression of Vm-milR16, but not mutated Vm-milR16, significantly reduces the expression of targets and virulence of V. mali. Furthermore, deletion of VmSNF1, VmDODA and VmHy1 significantly reduce virulence of V. mali. All three targets seem to be essential for oxidative stress response and VmSNF1 is required for expression of pectinase genes during V. mali-host interaction. Our results demonstrate Vm-milRNAs contributing to the infection of V. mali on apple trees by adaptively regulating virulence genes.

Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches

Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade plant biomass. This variation is found at many levels and includes genomic adaptation to the preferred biomass component, but also different approaches to degrade this component by diverse sets of activities encoded in the genome. Even larger differences have been observed using transcriptome and proteome studies, even between closely related species, suggesting a high level of adaptation in individual species. A better understanding of the drivers of this diversity could be highly valuable in developing more efficient biotechnology approaches for the enzymatic conversion of plant biomass.

Blistering1 Modulates Penicillium expansum Virulence Via Vesicle-mediated Protein Secretion

The blue mold fungus, Penicillium expansum, is a postharvest apple pathogen that contributes to food waste by rotting fruit and by producing harmful mycotoxins (e.g. patulin). To identify genes controlling pathogen virulence, a random T-DNA insertional library was created from wild-type P. expansum strain R19. One transformant, T625, had reduced virulence in apples, blistered mycelial hyphae, and a T-DNA insertion that abolished transcription of the single copy locus in which it was inserted. The gene, Blistering1, encodes a protein with a DnaJ domain, but otherwise has little homology outside the Aspergillaceae, a family of fungi known for producing antibiotics, mycotoxins, and cheese. Because protein secretion is critical for these processes and for host infection, mass spectrometry was used to monitor proteins secreted into liquid media during fungal growth. T625 failed to secrete a set of enzymes that degrade plant cell walls, along with ones that synthesize the three final biosynthetic steps of patulin. Consequently, the culture broth of T625 had significantly reduced capacity to degrade apple tissue and contained 30 times less patulin. Quantitative mass spectrometry of 3,282 mycelial proteins revealed that T625 had altered cellular networks controlling protein processing in the endoplasmic reticulum, protein export, vesicle-mediated transport, and endocytosis. T625 also had reduced proteins controlling mRNA surveillance and RNA processing. Transmission electron microscopy of hyphal cross sections confirmed that T625 formed abnormally enlarged endosomes or vacuoles. These data reveal that Blistering1 affects internal and external protein processing involving vesicle-mediated transport in a family of fungi with medical, commercial, and agricultural importance.

A PAS-Containing Histidine Kinase is Required for Conidiation, Appressorium Formation, and Disease Development in the Rice Blast Fungus, Magnaporthe oryzae

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most important diseases in rice production. PAS (period circadian protein, aryl hydrocarbon receptor nuclear translocator protein, single-minded protein) domains are known to be involved in signal transduction pathways, but their functional roles have not been well studied in fungi. In this study, targeted gene deletion was carried out to investigate the functional roles of the PAS-containing gene MoPAS1 (MGG_02665) in M. oryzae. The deletion mutant ΔMopas1 exhibited easily wettable mycelia, reduced conidiation, and defects in appressorium formation and disease development compared to the wild type and complemented transformant. Exogenous cAMP restored appressorium formation in ΔMopas1, but the shape of the restored appressorium was irregular, indicating that MoPAS1 is involved in sensing the hydrophobic surface. To examine the expression and localization of MoPAS1 in M. oryzae during appressorium development and plant infection, we constructed a MoPAS1:GFP fusion construct. MoPAS1:GFP was observed in conidia and germ tubes at 0 and 2 h post-infection (hpi) on hydrophobic cover slips. By 8 hpi, most of the GFP signal was observed in the appressoria. During invasive growth in host cells, MoPAS1:GFP was found to be fully expressed in not only the appressoria but also invasive hyphae, suggesting that MoPAS may contribute to disease development in host cells. These results expand our knowledge of the roles of PAS-containing regulatory genes in the plant-pathogenic fungus M. oryzae.

Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors

The study of pathogenic agents in their natural niches allows for a better understanding of disease persistence and dissemination. Bacteria belonging to the Agrobacterium genus are soil-borne and can colonize the rhizosphere. These bacteria are also well known as phytopathogens as they can cause tumors (crown gall disease) by transferring a DNA region (T-DNA) into a wide range of plants. Most reviews on Agrobacterium are focused on virulence determinants, T-DNA integration, bacterial and plant factors influencing the efficiency of genetic transformation. Recent research papers have focused on the plant tumor environment on the one hand, and genetic traits potentially involved in bacterium-plant interactions on the other hand. The present review gathers current knowledge about the special conditions encountered in the tumor environment along with the Agrobacterium genetic determinants putatively involved in bacterial persistence inside a tumor. By integrating recent metabolomic and transcriptomic studies, we describe how tumors develop and how Agrobacterium can maintain itself in this nutrient-rich but stressful and competitive environment.

A Rab GTPase protein FvSec4 is necessary for fumonisin B1 biosynthesis and virulence in Fusarium verticillioides

Rab GTPases are responsible for a variety of membrane trafficking and vesicular transportation in fungi. But the role of Rab GTPases in Fusarium verticillioides, one of the key corn pathogens worldwide, remains elusive. These Small GTPases in fungi, particularly those homologous to Saccharomyces cerevisiae Sec4, are known to be associated with protein secretion, vesicular trafficking, secondary metabolism and pathogenicity. In this study, our aim was to investigate the molecular functions of FvSec4 in F. verticillioides associated with physiology and virulence. Interestingly, the FvSec4 null mutation did not impair the expression of key conidiation-related genes. Also, the mutant did not show any defect in sexual development, including perithecia production. Meanwhile, GFP-FvSec4 localized to growing hyphal tips and raised the possibility that FvSec4 is involved in protein trafficking and endocytosis. The mutant exhibited defect in corn stalk rot virulence and also significant alteration of fumonisin B1 production. The mutation led to higher sensitivity to oxidative and cell wall stress agents, and defects in carbon utilization. Gene complementation fully restored the defects in the mutant demonstrating that FvSec4 plays important roles in these functions. Taken together, our data indicate that FvSec4 is critical in F. verticillioides hyphal development, virulence, mycotoxin production and stress responses.

Trichoderma harzianum Improves Defense Against Fusarium oxysporum by Regulating ROS and RNS Metabolism, Redox Balance, and Energy Flow in Cucumber Roots

Plant survival in the terrestrial ecosystem is influenced by both beneficial and harmful microbes. Trichoderma spp. are a group of filamentous fungi that promote plant growth and resistance to harmful microbes. Previously, we showed that the genus Trichoderma could effectively suppress Fusarium wilt in cucumber. However, the mechanisms that underlie the effects of the genus Trichoderma on plant defense have not been fully substantiated. Two essential metabolic pathways, such as the ascorbate (AsA)-glutathione (GSH) cycle and the oxidative pentose phosphate pathway (OPPP), have been shown to participate in plant tolerance to biotic stressors; nevertheless, the involvement of these pathways in Trichoderma-induced enhanced defense remains elusive. Here, we show that Trichoderma harzianum could alleviate oxidative and nitrostative stress by minimizing reactive oxygen species (ROS; hydrogen peroxide and superoxide) and reactive nitrogen species (nitric oxide [NO]) accumulation, respectively, under Fusarium oxysporum infection in cucumber roots. The genus Trichoderma enhanced antioxidant potential to counterbalance the overproduced ROS and attenuated the transcript and activity of NO synthase and nitrate reductase. The genus Trichoderma also stimulated S-nitrosylated glutathione reductase activity and reduced S-nitrosothiol and S-nitrosylated glutathione content. Furthermore, the genus Trichoderma enhanced AsA and GSH concentrations and activated their biosynthetic enzymes, γ-GCS and l-galactono-1,4-lactone dehydrogenase. Interestingly, the genus Trichoderma alleviated Fusarium-inhibited activity of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase, enzymes involved in the OPPP. Such positive regulation of the key enzymes indicates the adequate maintenance of the AsA-GSH pathway and the OPPP, which potentially contributed to improve redox balance, energy flow, and defense response. Our study advances the current knowledge of Trichoderma-induced enhanced defense against F. oxysporum in cucumber.

Highly flexible infection programs in a specialized wheat pathogen

Many filamentous plant pathogens exhibit high levels of genomic variability, yet the impact of this variation on host-pathogen interactions is largely unknown. We have addressed host specialization in the wheat pathogen Zymoseptoria tritici. Our study builds on comparative analyses of infection and gene expression phenotypes of three isolates and reveals the extent to which genomic variation translates into phenotypic variation. The isolates exhibit genetic and genomic variation but are similarly virulent. By combining confocal microscopy, disease monitoring, staining of ROS, and comparative transcriptome analyses, we conducted a detailed comparison of the infection processes of these isolates in a susceptible wheat cultivar. We characterized four core infection stages: establishment, biotrophic growth, lifestyle transition, and necrotrophic growth and asexual reproduction that are shared by the three isolates. However, we demonstrate differentiated temporal and spatial infection development and significant differences in the expression profiles of the three isolates during the infection stages. More than 20% of the genes were differentially expressed and these genes were located significantly closer to transposable elements, suggesting an impact of epigenetic regulation. Further, differentially expressed genes were enriched in effector candidates suggesting that isolate-specific strategies for manipulating host defenses are present in Z. tritici. We demonstrate that individuals of a host-specialized pathogen have highly differentiated infection programs characterized by flexible infection development and functional redundancy. This illustrates how high genetic diversity in pathogen populations results in highly differentiated infection phenotypes, which fact needs to be acknowledged to understand host-pathogen interactions and pathogen evolution.

A method to measure redox potential (Eh) and pH in agar media and plants shows that fungal growth is affected by and affects pH and Eh

The specificities of the plant environment and its effects on fungal growth are not yet fully explored. Both pH and Eh play a key role during this interaction, but are often studied independently or at different scales. We aimed at investigating whether the methods developed for the joint characterization of the pH and Eh in soil could be transposed to fungi. On artificial media, the growth of all 16 species tested significantly altered either Eh, pH or both. Measuring Eh reveals that even the species not modifying pH can have an impact on the surrounding environment. Reciprocally, fungi responded to pH and Eh parameters, both quantitatively with a decrease in colony diameter and qualitatively with colony aspect repeatedly and thoroughly modified. In infected oilseed rape plant stems, pH and Eh were significantly altered. The observed alcalinisation or acidification correlates with canker length. The joint characterization of both parameters will allow understanding the impact of fungi on their environment, and conversely of the environment on fungal growth. The availability of methods for measurement opens the prospect to study combinations of stresses, and get an understanding of the involvement of pH and Eh modifications in these interactions.

Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test

Plant genotype drives the development of plant phenotypes and the assembly of plant microbiota. The potential influence of the plant phenotypic characters on its microbiota is not well characterized and the co-occurrence interrelations for specific microbial taxa and plant phenotypic characters are poorly understood. We established a common garden experiment, which quantifies prokaryotic and fungal communities in the phyllosphere and rhizosphere of six spruce (Picea spp.) tree species, through Illumina amplicon sequencing. We tested for relationships between bacterial/archaeal and fungal communities and for the phenotypic characters of their plant hosts. Host phenotypic characters including leaf length, leaf water content, leaf water storage capacity, leaf dry mass per area, leaf nitrogen content, leaf phosphorous content, leaf potassium content, leaf δ¹³C values, stomatal conductance, net photosynthetic rate, intercellular carbon dioxide concentration, and transpiration rate were significantly correlated with the diversity and composition of the bacterial/archaeal and fungal communities. These correlations between plant microbiota and suites of host plant phenotypic characters suggest that plant genotype shape its microbiota by driving the development of plant phenotypes. This will advance our understanding of plant-microbe associations and the drivers of variation in plant and ecosystem function.

Pyramiding of nine transgenes in maize generates high-level resistance against necrotrophic maize pathogens

Key message Nine transgenes from different categories, viz. plant defense response genes and anti-apoptosis genes, played combined roles in maize to inhibit the necrotrophic pathogens Rhizoctonia solani and Bipolaris maydis. Maize sheath blight and southern corn leaf blight are major global threats to maize production. The management of these necrotrophic pathogens has encountered limited success due to the characteristics of their lifestyle. Here, we presented a transgenic pyramiding breeding strategy to achieve nine different resistance genes integrated in one transgenic maize line to combat different aspects of necrotrophic pathogens. These nine genes, selected from two different categories, plant defense response genes (Chi, Glu, Ace-AMP1, Tlp, Rs-AFP2, ZmPROPEP1 and Pti4), and anti-apoptosis genes (Iap and p35), were successfully transferred into maize and further implicated in resistance against the necrotrophic pathogens Rhizoctonia solani and Bipolaris maydis. Furthermore, the transgenic maize line 910, with high expression levels of the nine integrated genes, was selected from 49 lines. Under greenhouse and field trial conditions, line 910 showed significant resistance against maize sheath blight and southern corn leaf blight diseases. Higher-level resistance was obtained after the pyramiding of more resistance transgenes from different categories that function via different mechanisms. The present study provides a successful strategy for the management of necrotrophic pathogens.

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

Cultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, many of which have been identified. On the pathogen side, however, the molecular determinants of specificity remain largely unknown. We used genetic mapping, targeted gene disruption and allele swapping to characterise the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to characterise the evolutionary trajectory of Avr3D1. Avr3D1 is specifically recognised by wheat cultivars harbouring the Stb7 resistance gene, triggering a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a genome region populated by independent transposable element insertions. The gene was present in all 132 investigated strains and is highly polymorphic, with 30 different protein variants identified. We demonstrated that specific amino acid substitutions in Avr3D1 led to evasion of recognition. These results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive. Localising avirulence genes in highly plastic genomic regions probably facilitates accelerated evolution that enables escape from recognition by resistance proteins.

The role of water in plant-microbe interactions

Throughout their life plants are associated with various microorganisms, including commensal, symbiotic and pathogenic microorganisms. Pathogens are genetically adapted to aggressively colonize and proliferate in host plants to cause disease. However, disease outbreaks occur only under permissive environmental conditions. The interplay between host, pathogen and environment is famously known as the 'disease triangle'. Among the environmental factors, rainfall events, which often create a period of high atmospheric humidity, have repeatedly been shown to promote disease outbreaks in plants, suggesting that the availability of water is crucial for pathogenesis. During pathogen infection, water-soaking spots are frequently observed on infected leaves as an early symptom of disease. Recent studies have shown that pathogenic bacteria dedicate specialized virulence proteins to create an aqueous habitat inside the leaf apoplast under high humidity. Water availability in the apoplastic environment, and probably other associated changes, can determine the success of potentially pathogenic microbes. These new findings reinforce the notion that the fight over water may be a major battleground between plants and pathogens. In this article, we will discuss the role of water availability in host-microbe interactions, with a focus on plant-bacterial interactions.