Abstract
Viroids, minimalist plant pathogens, pose significant threats to crops by causing severe diseases. Transcriptome profiling technologies have significantly advanced the analysis of viroid-infected host plants, providing critical insights into gene regulation by these pathogens. Despite these advancements, the presence of numerous genes of unknown function continues to limit a complete understanding of the transcriptome data. Co-expression analysis addresses this issue by clustering genes into modules based on global gene expression levels, with genes in the same cluster likely participating in the same biological pathways. In a previous study, we emphasized the importance of basic helix-loop-helix (bHLH) proteins in transcriptional reprogramming in tomato host in response to different potato spindle tuber viroid (PSTVd) strains. In the current research, we delve into tissue-specific gene modules, particularly in root and leaf tissues, governed by bHLH transcription factors (TFs) during PSTVd infections. Utilizing public datasets that span Control (C), mock-inoculated, PSTVd-mild (M), and PSTVd-severe (S23) strains in time-course infections, we uncovered differentially expressed gene modules. These modules were functionally characterized to identify essential hub genes, notably highlighting the regulatory coordination of bHLH TFs, depicted through the significant bifan motif found in these interactions. Expanding on these findings, we explored bipartite networks, discerning both common and unique bHLH TF regulatory roles. Our findings reveal that bHLH TFs play pivotal roles in regulating processes such as energy metabolism and facilitating rapid membrane repair in infected roots. In leaves, changes in the external layers affected photosynthesis, linking bHLH TFs to distinct metabolic functions. Through this holistic approach, we deepen our understanding of viroid-host interactions and the intricate regulatory mechanisms underpinning them.