Author : Isip, Miguelito F.

Summary : Fungal pathogens persistently develop different strategies to circumvent plant defenses so that they can attack and enter their host. Botrytis cinerea is a devastating necrotrophic pathogen of tomato. However, most previous studies have explored limited infection stages, and the response at the pathogen end still remains largely uninvestigated. Therefore, this study aimed to analyze high-quality pathogen-enriched mixed-transcriptome at five infection stages of tomato leaves. Ortholog analysis between tomato and rice was also carried out to identify the conserved and non-conserved plant-host responses when host plants were infected with a fungal pathogen. As a result, several differentially expressed genes (DEGs) related to pathogen response in tomato were observed at 23, 40, and 47 hours post-infection (hpi); 144 DEG's were found, and 2.6% were constantly expressed across three time points. While tomato DEGs encoding disease-resistance proteins, receptor-like kinases, and pathogenesis-related proteins associated to jasmonic acid (JA) and ethylene (ET)-mediated responses, some virulence-and growth-related genes as well as candidate effectors were expressed in B. cinerea. Interestingly, the fungus expressed some defense-related genes for redox reaction and detoxification. Thus, it is suggested that the pathogen response is not completely passive, but rather exhibits an active defense strategy, potentially involving modulation of host defense responses or secretion of counteracting effectors. In addition, comparative transcriptome analysis revealed that 84% of the orthologous DEGs were highly conserved between tomato and rice, and 10.23% of which showed functional importance related to pathogen defense response. Moreover, cis-regulatory elements enrichment and deep learning analysis with the IDCNN model and guided-backpropagation identified WRKY and ERF as relevant regulatory motifs associated with biotic stress-responsive expression patterns in tomato. Furthermore, the large-scale comparative analysis of transcription start sites (TSS) in tomato and rice revealed intriguing patterns. A positive correlation was found between gene expression levels and both GC-skew and AT-skew, indicating that the nucleotide composition around the TSS may exert influence on gene expression. While both species exhibited conserved regulatory elements, such as the TATA box in the upstream TSS, variations were observed in the downstream regions. Specifically, rice displayed Y-patch signals that were absent in tomato. These findings suggest the involvement of specialized systems and distinct regulatory elements in the downstream transcriptional regulation, contributing to the diversity of TSS in plant genomes.