Sugar Partitioning between Ustilago maydis and Its Host Zea mays L during Infection

Maize requires arogenate dehydratase 2 for resistance to Ustilago maydis and plant development

Maize (Zea mays) smut is a common biotrophic fungal disease caused by Ustilago maydis and leads to low maize yield. Maize resistance to U. maydis is a quantitative trait. However, the molecular mechanism underlying the resistance of maize to U. maydis is poorly understood. Here, we reported that a maize mutant caused by a single gene mutation exhibited defects in both fungal resistance and plant development. maize mutant highly susceptible to U. maydis (mmsu) with a dwarf phenotype forms tumors in the ear. A map-based cloning and allelism test demonstrated that 1 gene encoding a putative arogenate dehydratase/prephenate dehydratase (ADT/PDT) is responsible for the phenotypes of the mmsu and was designated as ZmADT2. Combined transcriptomic and metabolomic analyses revealed that mmsu had substantial differences in multiple metabolic pathways in response to U. maydis infection compared with the wild type. Disruption of ZmADT2 caused damage to the chloroplast ultrastructure and function, metabolic flux redirection, and reduced the amounts of salicylic acid (SA) and lignin, leading to susceptibility to U. maydis and dwarf phenotype. These results suggested that ZmADT2 is required for maintaining metabolic flux, as well as resistance to U. maydis and plant development in maize. Meanwhile, our findings provided insights into the maize response mechanism to U. maydis infection.

Redundant and Distinct Roles of Two 14-3-3 Proteins in Fusarium sacchari, Pathogen of Sugarcane Pokkah Boeng Disease

Fusarium sacchari, a key pathogen of sugarcane, is responsible for the Pokkah boeng disease (PBD) in China. The 14-3-3 proteins have been implicated in critical developmental processes, including dimorphic transition, signal transduction, and carbon metabolism in various phytopathogenic fungi. However, their roles are poorly understood in F. sacchari. This study focused on the characterization of two 14-3-3 protein-encoding genes, FsBmh1 and FsBmh2, within F. sacchari. Both genes were found to be expressed during the vegetative growth stage, yet FsBmh1 was repressed at the sporulation stage in vitro. To elucidate the functions of these genes, the deletion mutants ΔFsBmh1 and ΔFsBmh2 were generated. The ΔFsBmh2 exhibited more pronounced phenotypic defects, such as impaired hyphal branching, septation, conidiation, spore germination, and colony growth, compared to the ΔFsBmh1. Notably, both knockout mutants showed a reduction in virulence, with transcriptome analysis revealing changes associated with the observed phenotypes. To further investigate the functional interplay between FsBmh1 and FsBmh2, we constructed and analyzed mutants with combined deletion and silencing (ΔFsBmh/siFsBmh) as well as overexpression (O-FsBmh). The combinations of ΔFsBmh1/siFsBmh2 or ΔFsBmh2/siFsBmh1 displayed more severe phenotypes than those with single allele deletions, suggesting a functional redundancy between the two 14-3-3 proteins. Yeast two-hybrid (Y2H) assays identified 20 proteins with pivotal roles in primary metabolism or diverse biological functions, 12 of which interacted with both FsBmh1 and FsBmh2. Three proteins were specifically associated with FsBmh1, while five interacted exclusively with FsBmh2. In summary, this research provides novel insights into the roles of FsBmh1 and FsBmh2 in F. sacchari and highlights potential targets for PBD management through the modulation of FsBmh functions.

Genome-Wide Characterization of the Maize (Zea mays L.) WRKY Transcription Factor Family and Their Responses to Ustilago maydis

Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens.

Starving the enemy: how plant and microbe compete for sugar on the border

As the primary energy source for a plant host and microbe to sustain life, sugar is generally exported by Sugars Will Eventually be Exported Transporters (SWEETs) to the host extracellular spaces or the apoplast. There, the host and microbes compete for hexose, sucrose, and other important nutrients. The host and microbial monosaccharide transporters (MSTs) and sucrose transporters (SUTs) play a key role in the "evolutionary arms race". The result of this competition hinges on the proportion of sugar distribution between the host and microbes. In some plants (such as Arabidopsis, corn, and rice) and their interacting pathogens, the key transporters responsible for sugar competition have been identified. However, the regulatory mechanisms of sugar transporters, especially in the microbes require further investigation. Here, the key transporters that are responsible for the sugar competition in the host and pathogen have been identified and the regulatory mechanisms of the sugar transport have been briefly analyzed. These data are of great significance to the increase of the sugar distribution in plants for improvement in the yield.

Galactosyltransferase GhRFS6 interacting with GhOPR9 involved in defense against Verticillium wilt in cotton

The soil-borne fungus Verticillium dahliae causes Verticillium wilt (VW), one of the most devastating diseases of cotton. In a previous study showed that GhOPR9 played a positive role in resistance of cotton to VW through the regulation of the Jasmonic acid (JA) pathway. Furtherly, we also found that GhOPR9 interacted with a sucrose galactosyltransferase GhRFS6. Raffinose synthase (RFS) plays a key role in plant innate immunity, including the abiotic stress of drought, darkness. However, there were few reports on the effects of RFS on biotic stress. In this study, we verified the function of GhRFS6 to VW. The expression analysis showed that the GhRFS6 may be regulated by various stresses, and it was upregulated under Vd076 and Vd991 pressures. Inhibition of GhRFS6 expression, hydrogen peroxide (H₂O₂) content, lignin content, cell wall thickness and a series of defense responses were decreased, and the resistance of cotton to V. dahliae was decreased. In addition, this study showed that GhRFS6 has glycosyltransferase activity and can participate in the regulation of α-galactosidase activity and raffinose and inositol synthesis. And that galactose was accumulated in cotton roots after GhRFS6 silencing, which is beneficial for the colonization and growth of V. dahliae. Furthermore, overexpression of GhRFS6 in Arabidopsis thaliana enhanced plant resistance to V. dahliae. In GUS staining, the promoter expression position of GhRFS6 was also altered after V. dahliae infection. Meanwhile, GhRFS6 has also been shown to resist VW through the regulation of the JA pathway. These results suggest that GhRFS6 is a potential molecular target for improving cotton resistance to VW.

Apoplastic and vascular defences

The apoplast comprises the intercellular space between cell membranes, includes the xylem, and extends to the rhizoplane and the outer surfaces of the plant. The apoplast plays roles in different biological processes including plant immunity. This highly specialised space is often the first place where pathogen recognition occurs, and this then triggers the immune response. The immune response in the apoplast involves different mechanisms that restrict pathogen infection. Among these responses, secretion of different molecules like proteases, proteins related to immunity, small RNAs and secondary metabolites play important and often additive or synergistic roles. In addition, production of reactive oxygen species occurs to cause direct deleterious effects on the pathogen as well as reinforce the plant's immune response by triggering modifications to cell wall composition and providing additional defence signalling capabilities. The pool of available sugar in the apoplast also plays a role in immunity. These sugars can be manipulated by both interactors, pathogens gaining access to nutrients whilst the plant's responses restrict the pathogen's access to nutrients. In this review, we describe the latest findings in the field to highlight the importance of the apoplast in plant-pathogen interactions and plant immunity. We also indicate where new discoveries are needed.

Leveraging genomics to understand the broader role of fungal small secreted proteins in niche colonization and nutrition

The last few years have seen significant advances in the breadth of fungi for which we have genomic resources and our understanding of the biological mechanisms evolved to enable fungi to interact with their environment and other organisms. One field of research that has seen a paradigm shift in our understanding concerns the role of fungal small secreted proteins (SSPs) classified as effectors. Classically thought to be a class of proteins utilized by pathogenic microbes to manipulate host physiology in support of colonization, comparative genomic studies have demonstrated that mutualistic fungi and fungi not associated with a living host (i.e., saprotrophic fungi) also encode inducible effector and candidate effector gene sequences. In this review, we discuss the latest advances in understanding how fungi utilize these secreted proteins to colonize a particular niche and affect nutrition and nutrient cycles. Recent studies show that candidate effector SSPs in fungi may have just as significant a role in modulating hyphosphere microbiomes and in orchestrating fungal growth as they do in supporting colonization of a living host. We conclude with suggestions on how comparative genomics may direct future studies seeking to characterize and differentiate effector from other more generalized functions of these enigmatic secreted proteins across all fungal lifestyles.

Organic acids and glucose prime late-stage fungal biotrophy in maize

Many plant-associated fungi are obligate biotrophs that depend on living hosts to proliferate. However, little is known about the molecular basis of the biotrophic lifestyle, despite the impact of fungi on the environment and food security. In this work, we show that combinations of organic acids and glucose trigger phenotypes that are associated with the late stage of biotrophy for the maize pathogen Ustilago maydis. These phenotypes include the expression of a set of effectors normally observed only during biotrophic development, as well as the formation of melanin associated with sporulation in plant tumors. U. maydis and other hemibiotrophic fungi also respond to a combination of carbon sources with enhanced proliferation. Thus, the response to combinations of nutrients from the host may be a conserved feature of fungal biotrophy.

Infection by Moniliophthora perniciosa reprograms tomato Micro-Tom physiology, establishes a sink, and increases secondary cell wall synthesis

Witches' broom disease of cacao is caused by the pathogenic fungus Moniliophthora perniciosa. By using tomato (Solanum lycopersicum) cultivar Micro-Tom (MT) as a model system, we investigated the physiological and metabolic consequences of M. perniciosa infection to determine whether symptoms result from sink establishment during infection. Infection of MT by M. perniciosa caused reductions in root biomass and fruit yield, a decrease in leaf gas exchange, and down-regulation of photosynthesis-related genes. The total leaf area and water potential decreased, while ABA levels, water conductance/conductivity, and ABA-related gene expression increased. Genes related to sugar metabolism and those involved in secondary cell wall deposition were up-regulated upon infection, and the concentrations of sugars, fumarate, and amino acids increased. 14C-glucose was mobilized towards infected MT stems, but not in inoculated stems of the MT line overexpressing CYTOKININ OXIDASE-2 (35S::AtCKX2), suggesting a role for cytokinin in establishing a sugar sink. The up-regulation of genes involved in cell wall deposition and phenylpropanoid metabolism in infected MT, but not in 35S::AtCKX2 plants, suggests establishment of a cytokinin-mediated sink that promotes tissue overgrowth with an increase in lignin. Possibly, M. perniciosa could benefit from the accumulation of secondary cell walls during its saprotrophic phase of infection.

When SWEETs Turn Tweens: Updates and Perspectives

Sugar translocation between cells and between subcellular compartments in plants requires either plasmodesmata or a diverse array of sugar transporters. Interactions between plants and associated microorganisms also depend on sugar transporters. The sugars will eventually be exported transporter (SWEET) family is made up of conserved and essential transporters involved in many critical biological processes. The functional significance and small size of these proteins have motivated crystallographers to successfully capture several structures of SWEETs and their bacterial homologs in different conformations. These studies together with molecular dynamics simulations have provided unprecedented insights into sugar transport mechanisms in general and into substrate recognition of glucose and sucrose in particular. This review summarizes our current understanding of the SWEET family, from the atomic to the whole-plant level. We cover methods used for their characterization, theories about their evolutionary origins, biochemical properties, physiological functions, and regulation. We also include perspectives on the future work needed to translate basic research into higher crop yields.

The barley HvSTP13GR mutant triggers resistance against biotrophic fungi

High-yielding and stress-resistant crops are essential to ensure future food supply. Barley is an important crop to feed livestock and to produce malt, but the annual yield is threatened by pathogen infections. Pathogens can trigger an altered sugar partitioning in the host plant, which possibly leads to an advantage for the pathogen. Hampering these processes represents a promising strategy to potentially increase resistance. We analysed the response of the barley monosaccharide transporter HvSTP13 towards biotic stress and its potential use for plant protection. The expression of HvSTP13 increased on bacterial and fungal pathogen-associated molecular pattern (PAMP) application, suggesting a PAMP-triggered signalling that converged on the transcriptional induction of the gene. Promoter studies indicate a region that is probably targeted by transcription factors downstream of PAMP-triggered immunity pathways. We confirmed that the nonfunctional HvSTP13GR variant confers resistance against an economically relevant biotrophic rust fungus in barley. Our experimental setup provides basal prerequisites to further decode the role of HvSTP13 in response to biological stress. Moreover, in line with other studies, our experiments indicate that the alteration of sugar partitioning pathways, in a host-pathogen interaction, is a promising approach to achieve broad and durable resistance in plants.

Early infection response of fungal biotroph Ustilago maydis in maize

Common smut, caused by Ustilago maydis (DC.) Corda, is a destructive fungal disease of maize worldwide; it forms large tumors, reducing corn yield and quality. However, the molecular defense mechanism to common smut in maize remains unclear. The present study aimed to use a leading maize inbred line Ye478 to analyze the response to U. maydis inoculation. The histological and cytological analyses demonstrated that U. maydis grew gradually to the host cells 6 h post-inoculation (hpi). The samples collected at 0, 3, 6, and 12 hpi were analyzed to assess the maize transcriptomic changes in response to U. maydis. The results revealed differences in hormone signaling, glycometabolism, and photosynthesis after U. maydis infection; specific changes were detected in jasmonic acid (JA), salicylic acid (SA), ethylene (ET), and abscisic acid (ABA) signaling pathways, glycolysis/gluconeogenesis, and photosystems I and II, probably related to defense response. MapMan analysis demonstrated that the differentially expressed genes between the treatment and control groups were clustered into light reaction and photorespiration pathways. In addition, U. maydis inoculation induced chloroplast swelling and damage, suggesting a significant effect on the chloroplast activity and subsequent metabolic process, especially hexose metabolism. A further genetic study using wild-type and galactinol-sucrose galactosyltransferase (gsg) and yellow-green leaf-1 (ygl-1) mutants identified that these two U. maydis-induced genes negatively regulated defense against common smut in maize. Our measurements showed the pathogen early-invasion process, and the key pathways of both chlorophyll biosynthesis and sugar transportation were critical modified in the infected maize line, thereby throwing a light on the molecular mechanisms in the maize-U. maydis interaction.

Untargeted Metabolomic Investigation of Wheat Infected with Stinking Smut Tilletia caries

Tilletia caries infection of wheat (Triticum aestivum) has become an increasing problem in organic wheat agriculture throughout the world. Little is known about how this pathogen alters host metabolism to ensure a successful infection. We investigated how T. caries allocates resources from wheat for its growth over the life cycle of the pathogen. An untargeted metabolomics approach that combined gas chromatography time-of-flight mass spectrometry and ultraperformance liquid chromatography tandem mass spectrometry platforms was used to determine which primary or specialized metabolite pathways are targeted and altered during T. caries infection. We found that T. caries does not dramatically alter the global metabolome of wheat but instead alters key metabolites for its own nutrient uptake and to antagonize host defenses by reducing wheat's sweet immunity response and other related pathways. Our results highlight metabolic characteristics needed for selecting wheat varieties that are resistant to T. caries infection for organic agriculture. In addition, several wheat metabolites were identified that could be used in developing a diagnostic tool for early detection of T. caries infection.

The GhSWEET42 Glucose Transporter Participates in Verticillium dahliae Infection in Cotton

The SWEET (sugars will eventually be exported transporter) proteins, a family of sugar transporters, mediate sugar diffusion across cell membranes. Pathogenic fungi can acquire sugars from plant cells to satisfy their nutritional demands for growth and infection by exploiting plant SWEET sugar transporters. However, the mechanism underlying the sugar allocation in cotton plants infected by Verticillium dahliae, the causative agent of Verticillium wilt, remains unclear. In this study, observations of the colonization of cotton roots by V. dahliae revealed that a large number of conidia had germinated at 48-hour post-inoculation (hpi) and massive hyphae had appeared at 96 hpi. The glucose content in the infected roots was significantly increased at 48 hpi. On the basis of an evolutionary analysis, an association analysis, and qRT-PCR assays, GhSWEET42 was found to be closely associated with V. dahliae infection in cotton. Furthermore, GhSWEET42 was shown to encode a glucose transporter localized to the plasma membrane. The overexpression of GhSWEET42 in Arabidopsis thaliana plants led to increased glucose content, and compromised their resistance to V. dahliae. In contrast, knockdown of GhSWEET42 expression in cotton plants by virus-induced gene silencing (VIGS) led to a decrease in glucose content, and enhanced their resistance to V. dahliae. Together, these results suggest that GhSWEET42 plays a key role in V. dahliae infection in cotton through glucose translocation, and that manipulation of GhSWEET42 expression to control the glucose level at the infected site is a useful method for inhibiting V. dahliae infection.

Analysis of Soluble Sugar Content in Minute Quantities of Rice Tissues by GC-MS

Soluble sugars play key roles in plant growth, development, and adaption to the environment. Characterizing sugar content profiling of plant tissues promotes our understanding of the mechanisms underlying these plant processes. Several technologies have been developed to quantitate soluble sugar content in plant tissues; however, it is difficult with only minute quantities of plant tissues available. Here, we provide a detailed protocol for gas chromatography mass spectrometry (GC-MS)-based soluble sugar profiling of rice tissues that offers a good balance of sensitivity and reliability, and is considerably more sensitive and accurate than other reported methods. We summarize all the steps from sample collection and soluble sugar extraction to derivatization procedures of the soluble extracted sugars, instrumentation settings, and data analysis.

Identification and Characterization of Two Transmembrane Proteins Required for Virulence of Ustilago maydis

Smut fungi comprise a large group of biotrophic phytopathogens infecting important crops such as wheat and corn. Through the secretion of effector proteins, the fungus actively suppresses plant immune reactions and modulates its host's metabolism. Consequently, how soluble effector proteins contribute to virulence is already characterized in a range of phytopathogens. However, membrane-associated virulence factors have been much less studied to date. Here, we investigated six transmembrane (TM) proteins that show elevated gene expression during biotrophic development of the maize pathogen Ustilago maydis. We show that two of the six proteins, named Vmp1 and Vmp2 (virulence-associated membrane protein), are essential for the full virulence of U. maydis. The deletion of the corresponding genes leads to a substantial attenuation in the virulence of U. maydis. Furthermore, both are conserved in various related smuts and contain no domains of known function. Our biochemical analysis clearly shows that Vmp1 and Vmp2 are membrane-associated proteins, potentially localizing to the U. maydis plasma membrane. Mass photometry and light scattering suggest that Vmp1 mainly occurs as a monomer, while Vmp2 is dimeric. Notably, the large and partially unstructured C-terminal domain of Vmp2 is crucial for virulence while not contributing to dimerization. Taken together, we here provide an initial characterization of two membrane proteins as virulence factors of U. maydis.

Plasmodesmata play pivotal role in sucrose supply to Meloidogyne graminicola-caused giant cells in rice

On infection, plant-parasitic nematodes establish feeding sites in roots from which they take up carbohydrates among other nutrients. Knowledge on how carbohydrates are supplied to the nematodes' feeding sites is limited. Here, gene expression analyses showed that RNA levels of OsSWEET11 to OsSWEET15 were extremely low in both Meloidogyne graminicola (Mg)-caused galls and noninoculated roots. All the rice sucrose transporter genes, OsSUT1 to OsSUT5, were either down-regulated in Mg-caused galls compared with noninoculated rice roots or had very low transcript abundance. OsSUT1 was the only gene up-regulated in galls, at 14 days postinoculation (dpi), after being highly down-regulated at 3 and 7 dpi. OsSUT4 was down-regulated at 3 dpi. No noticeable OsSUTs promoter activities were detected in Mg-caused galls of pOsSUT1 to -5::GUS rice lines. Loading experiments with carboxyfluorescein diacetate (CFDA) demonstrated that symplastic connections exist between phloem and Mg-caused giant cells (GCs). According to data from OsGNS5- and OsGSL2-overexpressing rice plants that had decreased and increased callose deposition, respectively, callose negatively affected Mg parasitism and sucrose supply to Mg-caused GCs. Our results suggest that plasmodesmata-mediated sucrose transport plays a pivotal role in sucrose supply from rice root phloem to Mg-caused GCs, and OsSWEET11 to -15 and OsSUTs are not major players in it, although further functional analysis is needed for OsSUT1 and OsSUT4.

How Do Smut Fungi Use Plant Signals to Spatiotemporally Orientate on and In Planta?

Smut fungi represent a large group of biotrophic plant pathogens that cause extensive yield loss and are also model organisms for studying plant-pathogen interactions. In recent years, they have become biotechnological tools. After initial penetration of the plant epidermis, smut fungi grow intra-and intercellularly without disrupting the plant-plasma membrane. Following the colonialization step, teliospores are formed and later released. While some smuts only invade the tissues around the initial penetration site, others colonize in multiple plant organs resulting in spore formation distal from the original infection site. The intimate contact zone between fungal hyphae and the host is termed the biotrophic interaction zone and enables exchange of signals and nutrient uptake. Obviously, all steps of on and in planta growth require fine sensing of host conditions as well as reprogramming of the host by the smut fungus. In this review, we highlight selected examples of smut fungal colonization styles, directional growth in planta, induction of spore formation, and the signals required, pointing to excellent reviews for details, to draw attention to some of the open questions in this important research field.

Understanding Ustilago maydis Infection of Multiple Maize Organs

Ustilago maydis is a smut fungus that infects all aerial maize organs, namely, seedling leaves, tassels, and ears. In all organs, tumors are formed by inducing hypertrophy and hyperplasia in actively dividing cells; however, the vast differences in cell types and developmental stages for different parts of the plant requires that U. maydis have both general and organ-specific strategies for infecting maize. In this review, we summarize how the maize–U. maydis interaction can be studied using mutant U. maydis strains to better understand how individual effectors contribute to this interaction, either through general or specific expression in a cell type, tissue, or organ. We also examine how male sterile maize mutants that do not support tumor formation can be used to explore key features of the maize anthers that are required for successful infection. Finally, we discuss key unanswered questions about the maize–U. maydis interaction and how new technologies can potentially be used to answer them.

Outstanding questions in flower metabolism

The great diversity of flowers, their color, odor, taste, and shape, is mostly a result of the metabolic processes that occur in this reproductive organ when the flower and its tissues develop, grow, and finally die. Some of these metabolites serve to advertise flowers to animal pollinators, other confer protection towards abiotic stresses, and a large proportion of the molecules of the central metabolic pathways have bioenergetic and signaling functions that support growth and the transition to fruits and seeds. Although recent studies have advanced our general understanding of flower metabolism, several questions still await an answer. Here, we have compiled a list of open questions on flower metabolism encompassing molecular aspects, as well as topics of relevance for agriculture and the ecosystem. These questions include the study of flower metabolism through development, the biochemistry of nectar and its relevance to promoting plant-pollinator interaction, recycling of metabolic resources after flowers whiter and die, as well as the manipulation of flower metabolism by pathogens. We hope with this review to stimulate discussion on the topic of flower metabolism and set a reference point to return to in the future when assessing progress in the field.

Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.