Transcriptomic Profiling of Host Responses Underlying Synergistic Interaction Between the Phloem-Limited Brassica Yellows Virus and Pea Enation Mosaic Virus 2 in Nicotiana benthamiana

Phloem-restricted poleroviruses cause substantial yield losses in crops. Co-infection of the polerovirus brassica yellows virus (BrYV) with the umbravirus pea enation mosaic virus 2 (PEMV 2) results in synergistic interactions that enable BrYV to overcome phloem limitation in <i>Nicotiana benthamiana</i>, yet the associated host transcriptional responses remain poorly understood. At 7 days post inoculation (dpi), BrYV RNA accumulation was increased in plants co-infected with BrYV and PEMV 2, although no visible symptoms or detectable cell death were observed. By 14 dpi, extensive cell death was induced in upper leaves infected with BrYV and PEMV 2. Transcriptome analysis at 14 dpi identified 45, 188, and 1962 differentially expressed genes (DEGs) in leaves infected with BrYV, PEMV 2, and co-infected with BrYV and PEMV 2, respectively, compared with mock-inoculated plants. A large number of DEGs, Gene Ontology terms, and KEGG pathways were predominantly observed in co-infected plants. Notably, expression changes were observed in genes related to plasmodesmata-associated processes, RNA silencing, photosynthesis, cell death, and ethylene biosynthesis and signaling during co-infection. These results provide a transcriptome-based overview of host responses during the late stage of BrYV and PEMV 2 co-infection and highlight the complexity of viral synergism between phloem-limited and taxonomically distinct plant viruses.