Comprehensive Lipidomic and Transcriptomic Analysis of Arabidopsis upon Verticillium dahliae Infection.

Distinct lipid and hormonal signatures reveal divergent responses to Erysiphe necator in resistant and susceptible grapevine genotypes

Key metabolic, signalling and gene expression features in the selected hybrid that may be relevant for resistance are identified, including rapid triacylglycerols degradation, galactolipid peroxidation, constitutive higher SA level and expression of the defensin VviAMP1.

Functional Analysis of Spinach Downy Mildew Effectors

Plants are susceptible to microbial infections that can cause disease and severe yield losses. Although plant–microbe interactions have been extensively studied in model systems, translating this knowledge into improved disease resistance in crops remains challenging, especially for non-model pathosystems with limited biological understanding and experimental tools. One such system is spinach downy mildew, caused by the obligate biotrophic oomycete Peronospora effusa (P. effusa). This rapidly evolving pathogen readily overcomes newly deployed resistance traits in spinach, highlighting the need for novel and more durable resistance. A deeper understanding of the P. effusa–spinach interaction may provide new leads to support the development of new pest management strategies. In chapter 2, we investigated how P. effusa deploys its gene repertoire during infection. Using time-resolved transcriptomic profiling across the complete asexual infection cycle, we show that P. effusa undergoes extensive and coordinated gene expression reprogramming associated with major developmental transitions. These changes involve stress responses, signalling pathways, metabolism, macromolecule biosynthesis, and distinct waves of effector expression. Several predicted virulence factors, including effectors, localise to genomic regions resembling pathogenicity islands and display coordinated expression patterns, suggesting that genome architecture contributes to the regulation of virulence. To enable functional studies in spinach, chapters 3 and 4 focus on establishing bacterial platforms for effector analysis in planta. In chapter 3, I evaluate Agrobacterium-mediated transient gene expression in spinach. Although reporter genes, including RUBY, could be expressed, expression levels were low and variable, and the absence of cell death responses indicated that further optimisation is required before this system can be used for resistance gene discovery. In chapter 4, I explored an alternative approach based on Type III Secretion System-mediated effector delivery. I identified Pseudomonas syringae pv. tomato DC3000 D36E, a strain lacking endogenous Type III effectors, as a suitable chassis for effector screening in spinach. Using this system, I assessed the effects of candidate effectors on disease symptoms, bacterial proliferation, and reactive oxygen species production, establishing the first deployable platform for functional effector studies in spinach. Together, this thesis advances understanding of P. effusa infection and provides both candidate virulence genes and experimental tools for functional studies, thereby supporting targeted and durable resistance breeding in spinach.

Transcriptomic and Metabolomic Analyses Reveal the Phenylpropanoid Metabolism Regulatory Network in Arabidopsis Response to Colletotrichum higginsianum Infection

Colletotrichum higginsianum (Ch) is a typical hemibiotrophic ascomycetous fungus. The diseases it causes often lead to considerable economic losses in global cruciferous crop production. However, current knowledge is still insufficient for us to gain a deeper understanding of how host plants respond at the transcriptional level during Ch infection. Herein, we performed transcriptomic and metabolic assays between Mock and Ch- infected samples. The results showed that Ch infection significantly inhibited the shoot fresh weight and primary root length of host plants. Furthermore, gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to phenylpropanoid metabolism were highly enriched. Defense hormone salicylic acid (SA) and three metabolites belonging to the phenylpropanoid metabolism pathway were identified. Meanwhile, we screened 5 related enzyme-encoding genes and 78 transcription factors (TFs). Five WRKY, three MYB, and two NAC TFs showed significant expression changes and high correlation with enzyme genes. Our results enrich regulatory networks in crucifier pathogen responses. This work provides potential molecular candidates to support subsequent studies on the mechanisms underlying Ch resistance.

Integrated Sphingolipidomic and Transcriptomic Analysis Reveals Resistance Mechanisms to Bacterial Wilt in Peanut Varieties with Contrasting Tolerance

This multi-omics framework provides detailed lipidomic and transcriptomic signatures to identify candidate genes and lipid biomarkers for marker-assisted breeding of bacterial wilt-resistant peanut varieties.

Transcriptomic and predictive modeling reveal photosynthetic and stress responses associated with ALAD silencing in citrus

Integrated Analysis of Transcriptomic and Metabolomic Responses in Rice Resisting False Smut