Plant susceptible responses: the underestimated side of plant-pathogen interactions

Soil-plant-gall relationships: from gall development to ecological patterns

The adaptive nature of the galler habit has been tentatively explained by the nutrition, microenvironment, and enemy hypotheses. Soil attributes have direct relationships with these three hypotheses at the cellular and macroecological scales, but their influence has been restricted previously to effects on the nutritional status of the host plant on gall richness and abundance. Herein, we discuss the ionome patterns within gall tissues and their significance for gall development, physiology, structure, and for the nutrition of the gallers. Previous ecological and chemical quantification focused extensively on nitrogen and carbon contents, evoking the carbon-nutrient defence hypothesis as an explanation for establishing the plant-gall interaction. Different elements are involved in cell wall composition dynamics, antioxidant activity, and regulation of plant-gall water dynamics. An overview of the different soil-plant-gall relationships highlights the complexity of the nutritional requirements of gallers, which are strongly influenced by environmental soil traits. Soil and plant chemical profiles interact to determine the outcome of plant-herbivore interactions and need to be addressed by considering not only the soil features and galler nutrition but also the host plant's physiological traits. The quantitative and qualitative results for iron metabolism in gall tissues, as well as the roles of iron as an essential element in the physiology and reproduction of gallers suggest that it may represent a key nutritional resource, aligning with the nutrition hypothesis, and providing an integrative explanation for higher gall diversity in iron-rich soils.

Comparative transcriptional analysis of Persea americana MYB, WRKY and AP2/ERF transcription factors following Phytophthora cinnamomi infection

Plant cells undergo extensive transcriptional reprogramming following pathogen infection, with these reprogramming patterns becoming more complex when pathogens, such as hemibiotrophs, exhibit different lifestyles. These transcriptional changes are often orchestrated by MYB, WRKY and AP2/ERF transcription factors (TFs), which modulate both growth and defence-related gene expression. Transcriptional analysis of defence-related genes in avocado (Persea americana) infected with Phytophthora cinnamomi indicated differential immune response activation when comparing a partially resistant and susceptible rootstock. This study identified 226 MYB, 82 WRKY, and 174 AP2/ERF TF-encoding genes in avocado, using a genome-wide approach. Phylogenetic analysis revealed substantial sequence conservation within TF groups underscoring their functional significance. RNA-sequencing analysis in a partially resistant and susceptible avocado rootstock infected with P. cinnamomi was indicative of an immune response switch occurring in either rootstock after 24 and 6 h post-inoculation, respectively. Different clusters of co-expressed TF genes were observed at these times, suggesting the activation of necrotroph-related immune responses at varying intervals between the two rootstocks. This study aids our understanding of avocado immune response activation following P. cinnamomi infection, and the role of the TFs therein, elucidating the transcriptional reprogramming disparities between partially resistant and susceptible rootstocks.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Svx Peptidases of Phytopathogenic Pectolytic Bacteria: Structural, Catalytic and Phytoimmune Properties

Svx proteins are virulence factors secreted by phytopathogenic bacteria of the Pectobacterium genus into the host plant cell wall. Svx-encoding genes are present in almost all species of the soft rot Pectobacteriaceae (Pectobacterium and Dickeya genera). The Svx of P. atrosepticum (Pba) has been shown to be a gluzincin metallopeptidase that presumably targets plant extensins, proteins that contribute to plant cell wall rigidity and participate in cell signaling. However, the particular "output" of the Pba Svx action in terms of plant-pathogen interactions and plant immune responses remained unknown. The Svx proteins are largely unexplored in Dickeya species, even though some of them have genes encoding two Svx homologs. Therefore, our study aims to compare the structural and catalytic properties of the Svx proteins of Pba and D. solani (Dso) and to test the phytoimmune properties of these proteins. Two assayed Dso Svx proteins, similar to Pba Svx, were gluzincin metallopeptidases with conservative tertiary structures. The two domains of the Svx proteins form electronegative clefts where the active centers of the peptidase domains are located. All three assayed Svx proteins possessed phytoimmunosuppressory properties and induced ethylene-mediated plant susceptible responses that play a decisive role in Pba-caused disease.

Characterization of heteropolysaccharides from Rhizoctonia solani AG1 IA cell wall and comparison of their effect on inducing plant defense

Rhizoctonia solani (R. solani) is an important pathogenic fungus that causes symptoms of sheath blight, and the polysaccharide-rich cell wall plays a major role in plant-pathogen interactions. However, the composition and structure of its cell wall polysaccharides are insufficiently understood, and its specific function in plant-pathogen interactions is unknown, which makes effective control of sheath blight difficult at present. Herein, five cell wall polysaccharides (WF-1, WF-2, CAF-1, HAF-1 and HAF 2-1) were sequentially extracted by boiling water, cold and hot alkali from R. solani AG1 IA. They were heteropolysaccharides containing mainly glucose, mannose and galactose and less fucose, with molecular weights above 1100 kDa. These five polysaccharides mainly composed of →4)-Glcp-(1→, →6)-Glcp-(1→, →4,6)-Glcp-(1→, →3,4)-Glcp-(1→, and Manp-(1→. Several polysaccharides, except WF-1, showed different induced resistance degrees on rice plant, with HAF 2-1 having the most significant effect. Further analysis using NMR confirmed that the backbone of HAF 2-1 mainly consisted of →4)-α-D-Glcp-(1→ and →6)-α-D-Glcp-(1→ with branches of →4,6)-D-Glcp-(1→. HAF 2-1 enhance the resistance of rice against R. solani through salicylic acid (SA)-mediated immune signaling pathway. This work improves our knowledge of the cell wall polysaccharides in plant pathogens and facilitates the study of pathogenic mechanisms and effective disease control.

Advances in understanding the mechanism of resistance to anthracnose and induced defence response in tea plants

The tea plant (Camellia sinensis) is susceptible to anthracnose disease that causes considerable crop loss and affects the yield and quality of tea. Multiple Colletotrichum spp. are the causative agents of this disease, which spreads quickly in warm and humid climates. During plant-pathogen interactions, resistant cultivars defend themselves against the hemibiotrophic pathogen by activating defence signalling pathways, whereas the pathogen suppresses plant defences in susceptible varieties. Various fungicides have been used to control this disease on susceptible plants, but these fungicide residues are dangerous to human health and cause fungicide resistance in pathogens. The problem-solving approaches to date are the development of resistant cultivars and ecofriendly biocontrol strategies to achieve sustainable tea cultivation and production. Understanding the infection stages of Colletotrichum, tea plant resistance mechanisms, and induced plant defence against Colletotrichum is essential to support sustainable disease management practices in the field. This review therefore summarizes the current knowledge of the identified causative agent of tea plant anthracnose, the infection strategies and pathogenicity of C. gloeosporioides, anthracnose disease resistance mechanisms, and the caffeine-induced defence response against Colletotrichum infection. The information reported in this review will advance our understanding of host-pathogen interactions and eventually help us to develop new disease control strategies.

A Switch from Latent to Typical Infection during Pectobacterium atrosepticum-Tobacco Interactions: Predicted and True Molecular Players

Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease management. No studies to date have compared, at the systemic molecular level, the physiological portraits of plants when different infection types (typical and latent) are developed. The only phytopathogenic bacterium for which latent infections were not only widely described but also at least fluently characterized at the molecular level is Pectobacterium atrosepticum (Pba). The present study aimed at the comparison of plant transcriptome responses during typical and latent infections caused by Pba in order to identify and then experimentally verify the key molecular players that act as switchers, turning peaceful plant-Pba coexistence into a typical infection. Based on RNA-Seq, we predicted plant cell wall-, secondary metabolism-, and phytohormone-related genes whose products contributed to the development of the disease or provided asymptomatic plant-Pba interactions. By treatment tests, we confirmed that a switch from latent to typical Pba-caused infection is determined by the plant susceptible responses mediated by the joint action of ethylene and jasmonates.

Economic versus technical efficiency in using ASM combined with fungicides to elicit wheat varieties with different disease susceptibilities

Despite the positive results of using elicitors to induce resistance against plant diseases, some factors have inhibited the popularization of their use in agriculture. There is an energetic cost related to the elicitors' induced response which can cause undesired effects on growth under low-pressure disease conditions. Elicitors can create phytotoxicity and show high variation in their efficiency between different genotypes within the same crop; in addition, the positive results related to the induced resistance may not repeat in field treatments, adding to the possibility that they are not economically viable. Thus, we carried out two experiments to investigate the technical and economic efficiency of acibenzolar-S-methyl (ASM) and its association with fungicides in the control of leaf diseases of susceptible and resistant wheat varieties, and as how it reflects on the photosynthetic and production performance of wheat. This study showed the limitations of incorporating ASM into foliar fungal disease control in economic terms. However, it was evident that ASM effectively induced plant resistance against Leaf Rust and Powdery Mildew in the field and can be considered a sustainable option for wheat cultivation. Even though its association with chemical control was not the best economic strategy the use of ASM is a tool that can be incorporated into wheat cultivation to minimize the emergence of fungicide-resistant pathogens due to the diversification of modes of action employed and reduce the toxic residue deposition to the environment and human health.

First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale

Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.

Host plant physiological transformation and microbial population heterogeneity as important determinants of the Soft Rot Pectobacteriaceae-plant interactions

Pectobacterium and Dickeya species belonging to the Soft Rot Pectobacteriaceae (SRP) are one of the most devastating phytopathogens. They degrade plant tissues by producing an arsenal of plant cell wall degrading enzymes. However, SRP-plant interactions are not restricted to the production of these "brute force" weapons. Additionally, these bacteria apply stealth behavior related to (1) manipulation of the host plant via induction of susceptible responses and (2) formation of heterogeneous populations with functionally specialized cells. Our review aims to summarize current knowledge on SRP-induced plant susceptible responses and on the heterogeneity of SRP populations. The review shows that SRP are capable of adjusting the host's hormonal balance, inducing host-mediated plant cell wall modification, promoting iron assimilation by the host, stimulating the accumulation of reactive oxygen species and host cell death, and activating the synthesis of secondary metabolites that are ineffective in limiting disease progression. By this means, SRP facilitate host plant susceptibility. During host colonization, SRP populations produce various functionally specialized cells adapted for enhanced virulence, increased resistance, motility, vegetative growth, or colonization of the vascular system. This enables SRP to perform self-contradictory tasks, which benefits a population's overall fitness in various environments, including host plants. Such stealthy tactical actions facilitate plant-SRP interactions and disease progression.

Alterations in Primary Carbon Metabolism in Cucumber Infected with Pseudomonas syringae pv lachrymans: Local and Systemic Responses

The reconfiguration of the primary metabolism is essential in plant–pathogen interactions. We compared the local metabolic responses of cucumber leaves inoculated with Pseudomonas syringae pv lachrymans (Psl) with those in non-inoculated systemic leaves, by examining the changes in the nicotinamide adenine dinucleotides pools, the concentration of soluble carbohydrates and activities/gene expression of carbohydrate metabolism-related enzymes, the expression of photosynthesis-related genes, and the tricarboxylic acid cycle-linked metabolite contents and enzyme activities. In the infected leaves, Psl induced a metabolic signature with an altered [NAD(P)H]/[NAD(P)⁺] ratio; decreased glucose and sucrose contents, along with a changed invertase gene expression; and increased glucose turnover and accumulation of raffinose, trehalose, and myo-inositol. The accumulation of oxaloacetic and malic acids, enhanced activities, and gene expression of fumarase and l-malate dehydrogenase, as well as the increased respiration rate in the infected leaves, indicated that Psl induced the tricarboxylic acid cycle. The changes in gene expression of ribulose-l,5-bis-phosphate carboxylase/oxygenase large unit, phosphoenolpyruvate carboxylase and chloroplast glyceraldehyde-3-phosphate dehydrogenase were compatible with a net photosynthesis decline described earlier. Psl triggered metabolic changes common to the infected and non-infected leaves, the dynamics of which differed quantitatively (e.g., malic acid content and metabolism, glucose-6-phosphate accumulation, and glucose-6-phosphate dehydrogenase activity) and those specifically related to the local or systemic response (e.g., changes in the sugar content and turnover). Therefore, metabolic changes in the systemic leaves may be part of the global effects of local infection on the whole-plant metabolism and also represent a specific acclimation response contributing to balancing growth and defense.

Determination of Reactive Oxygen or Nitrogen Species and Novel Volatile Organic Compounds in the Defense Responses of Tomato Plants against Botrytis cinerea Induced by Trichoderma virens TRS 106

In the present study, Trichoderma virens TRS 106 decreased grey mould disease caused by Botrytis cinerea in tomato plants (S. lycopersicum L.) by enhancing their defense responses. Generally, plants belonging to the ‘Remiz’ variety, which were infected more effectively by B. cinerea than ‘Perkoz’ plants, generated more reactive molecules such as superoxide (O₂⁻) and peroxynitrite (ONOO⁻), and less hydrogen peroxide (H₂O₂), S-nitrosothiols (SNO), and green leaf volatiles (GLV). Among the new findings, histochemical analyses revealed that B. cinerea infection caused nitric oxide (NO) accumulation in chloroplasts, which was not detected in plants treated with TRS 106, while treatment of plants with TRS 106 caused systemic spreading of H₂O₂ and NO accumulation in apoplast and nuclei. SPME-GCxGC TOF-MS analysis revealed 24 volatile organic compounds (VOC) released by tomato plants treated with TRS 106. Some of the hexanol derivatives, e.g., 4-ethyl-2-hexynal and 1,5-hexadien-3-ol, and salicylic acid derivatives, e.g., 4-hepten-2-yl and isoamyl salicylates, are considered in the protection of tomato plants against B. cinerea for the first time. The results are valuable for further studies aiming to further determine the location and function of NO in plants treated with Trichoderma and check the contribution of detected VOC in plant protection against B. cinerea.

Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification

Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.

Gene expression and phytohormone levels in the asymptomatic and symptomatic phases of infection in potato tubers inoculated with Dickeya solani

Dickeya solani is a soft rot bacterium with high virulence. In potato, D. solani, like the other potato-infecting soft rot bacteria, causes rotting and wilting of the stems and rotting of tubers in the field and in storage. Latent, asymptomatic infections of potato tubers are common in harvested tubers, and if the storage conditions are not optimal, the latent infection turns into active rotting. We characterized potato gene expression in artificially inoculated tubers in nonsymptomatic, early infections 1 and 24 hours post-inoculation (hpi) and compared the results to the response in symptomatic tuber tissue 1 week (168 hpi) later with RNA-Seq. In the beginning of the infection, potato tubers expressed genes involved in the detection of the bacterium through pathogen-associated molecular patterns (PAMPs), which induced genes involved in PAMPs-triggered immunity, resistance, production of pathogenesis-related proteins, ROS, secondary metabolites and salicylic acid (SA) and jasmonic acid (JA) biosynthesis and signaling genes. In the symptomatic tuber tissue one week later, the PAMPs-triggered gene expression was downregulated, whereas primary metabolism was affected, most likely leading to free sugars fueling plant defense but possibly also aiding the growth of the pathogen. In the symptomatic tubers, pectic enzymes and cell wall-based defenses were activated. Measurement of hormone production revealed increased SA concentration and almost no JA in the asymptomatic tubers at the beginning of the infection and high level of JA and reduced SA in the symptomatic tubers one week later. These findings suggest that potato tubers rely on different defense strategies in the different phases of D. solani infection even when the infection takes place in fully susceptible plants incubated in conditions leading to rotting. These results support the idea that D. solani is a biotroph rather than a true necrotroph.

Seed Transmission of Pathogens: Non-Canonical Immune Response in Arabidopsis Germinating Seeds Compared to Early Seedlings against the Necrotrophic Fungus Alternaria brassicicola

The transmission of seed-borne pathogens by the germinating seed is responsible for major crop diseases. The immune responses of the seed facing biotic invaders are poorly documented so far. The Arabidopsis thaliana/Alternaria brassicicola patho-system was used to describe at the transcription level the responses of germinating seeds and young seedling stages to infection by the necrotrophic fungus. RNA-seq analyses of healthy versus inoculated seeds at 3 days after sowing (DAS), stage of radicle emergence, and at 6 and 10 DAS, two stages of seedling establishment, identified thousands of differentially expressed genes by Alternaria infection. Response to hypoxia, ethylene and indole pathways were found to be induced by Alternaria in the germinating seeds. However, surprisingly, the defense responses, namely the salicylic acid (SA) pathway, the response to reactive oxygen species (ROS), the endoplasmic reticulum-associated protein degradation (ERAD) and programmed cell death, were found to be strongly induced only during the latter post-germination stages. We propose that this non-canonical immune response in early germinating seeds compared to early seedling establishment was potentially due to the seed-to-seedling transition phase. Phenotypic analyses of about 14 mutants altered in the main defense pathways illustrated these specific defense responses. The unexpected germination deficiency and insensitivity to Alternaria in the glucosinolate deficient mutants allow hypothesis of a trade-off between seed germination, necrosis induction and Alternaria transmission to the seedling. The imbalance of the SA and jasmonic acid (JA) pathways to the detriment of the JA also illustrated a non-canonical immune response at the first stages of the seedling.

Structure-Functional Characteristics of the Svx Protein—The Virulence Factor of the Phytopathogenic Bacterium Pectobacterium atrosepticum

The Svx proteins are virulence factors of phytopathogenic bacteria of the Pectobacterium genus. The specific functions of these proteins are unknown. Here we show that most of the phytopathogenic species of Pectobacterium, Dickeya, and Xanthomonas genera have genes encoding Svx proteins, as well as some plant-non-associated species of different bacterial genera. As such, the Svx-like proteins of phytopathogenic species form a distinct clade, pointing to the directed evolution of these proteins to provide effective interactions with plants. To get a better insight into the structure and functions of the Svx proteins, we analyzed the Svx of Pectobacterium atrosepticum (Pba)—an extracellular virulence factor secreted into the host plant cell wall (PCW). Using in silico analyses and by obtaining and analyzing the recombinant Pba Svx and its mutant forms, we showed that this protein was a gluzincin metallopeptidase. The 3D structure model of the Pba Svx was built and benchmarked against the experimental overall secondary structure content. Structure-based substrate specificity analysis using molecular docking revealed that the Pba Svx substrate-binding pocket might accept α-glycosylated proteins represented in the PCW by extensins—proteins that strengthen the PCW. Thus, these results elucidate the way in which the Pba Svx may contribute to the Pba virulence.

Does Abiotic Host Stress Favour Dothideomycete-Induced Disease Development?

Dothideomycetes represent one of the largest and diverse class of fungi. This class exhibits a wide diversity of lifestyles, including endophytic, saprophytic, pathogenic and parasitic organisms. Plant pathogenic fungi are particularly common within the Dothideomycetes and are primarily found within the orders of Pleosporales, Botryosphaeriales and Capnodiales. As many Dothideomycetes can infect crops used as staple foods around the world, such as rice, wheat, maize or banana, this class of fungi is highly relevant to food security. In the context of climate change, food security faces unprecedented pressure. The benefits of a more plant-based diet to both health and climate have long been established, therefore the demand for crop production is expected to increase. Further adding pressure on food security, both the prevalence of diseases caused by fungi and the yield losses associated with abiotic stresses on crops are forecast to increase in all climate change scenarios. Furthermore, abiotic stresses can greatly influence the outcome of the host-pathogen interaction. This review focuses on the impact of abiotic stresses on the host in the development of diseases caused by Dothideomycete fungi.

Alterations in the Transcriptome of Rye Plants following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.