In summary, our results revealed that bHLH, ERF, and MYB TFs regulate gene expression in communities associated with unique biological processes, such as the valine, leucine, and isoleucine biosynthesis, vitamin B6 metabolism, anthocyanin biosynthesis, amino acid, and other molecules transmembrane transport, KEGG pathways, as well as participating together in the modulation of conserved crucial molecular processes, such as the C5-Branched dibasic acid metabolism, ribosome, photosynthesis, plant-pathogen interaction, and defense response in the PSTVd variants infection. Here, ERF is linked to infection.