Fusarium oxysporum causes devastating wilt diseases in more than one hundred crops. To provide a foundation for developing technologies to enhance plant health, sustain a healthy ecosystem, and feed a continuously growing human population, my dissertation research has focused on uncovering transcriptional responses and regulations during F. oxysporum and plant interactions from fungi and plant host aspects. Through a literature review (Chapter 1), we learned that accessory chromosomes (ACs) and transcriptional regulators are essential for the host-specific virulence of F. oxysporum. Transcription factors, key regulatory elements in the sensory and response networks of these fungi, undoubtedly play a fundamental role in establishing the adaptability of this group. We compared the TFome (Chapter 2), which consists of all TFs found within a genome, to look at a species' evolutionary history of its regulatory mechanisms. The study revealed both the conservation and diversity of F. oxysporum TFome. The ACs from each F. oxysporum genome likely dictate strain-specific interactions with a particular host. This allows a comparative study that minimizes genetic differences between strains to address the underlying mechanism that results in distinct phenotypes (e.g., pathogenic vs. non-pathogenic outcomes). We performed a comparative transcriptomics study (Chapter 3) of infection by an endophytic (Fo47) and a pathogenic (Fo5176) strain of F. oxysporum in the context of the F. oxysporum-Arabidopsis pathosystem, which revealed the transcriptional plasticity of plant defense responses. F. oxysporum penetrates the root epidermis, propagating and moving toward the vasculature. These pathogens' occupation of the vascular system blocks water and nutrient transport, further causing devastating wilt disease. Extensive efforts have been taken by bulk transcriptome profiling to probe the integral plant responses to the F. oxysporum stress. However, as the pathogen journeys through multiple layers to establish the infection, different root cell types likely respond differently. We performed a single-nucleus RNA sequencing analysis in the Arabidopsis-F. oxysporum pathosystem (Chapter 4). Our research revealed a unique pathogen-induced cell cluster enriched for defense-related functions that could aid in developing new strategies to improve plant defense mechanisms.