This dissertation is composed of two projects that focus on pathogen and plant signaling within the framework of plant pathology. The first project targets protein kinases within the species complex Fusarium oxysporum based on genomic information and tracks their presence/absence and copy number variation across evolutionary time. We have predicted the kinomes of 19 Ascomycete fungi using the kinase annotating software Kinannote. Among Fusaria, kinases related to the perception of the environment, such as Histidine kinases, are proliferated. Similarly, I observed the expansion of Target of Rapamycin (TOR) kinase that regulates cell growth and development in responding to environmental cues. The second project compares metatranscriptomics of a resistant (MRI) versus a susceptible (SB22) Ocimum basilicum) cultivars, both infected with the pathogen Peronospora belbahrii. Using de novo approach, I predicted MRI unique genes, including R-genes and malectin-domain containing receptor-like kinases and genes involved in the biosynthesis of plant secondary metabolites. Based on the observation of the unique upregulation of isochorismate synthase in MRI, I hypothesize that salicylic acid is involved in the resistance response of MRI.