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Cucumber mosaic virus (CMV) is among the most important plant virus infections, inducing a variety of disease symptoms. However, the molecular mechanisms underlying plant responses to CMV infection remain poorly understood. In this study, we performed RNA sequencing analysis of tolerant (Taiyan8) and susceptible (NC82) tobacco cultivars on CMV-infected plants, using mock-inoculated plants as a control. The propagation of CMV in inoculated leaves did not show obvious difference between two cultivars, whereas virus accumulation in systemic leaves of Taiyan8 was smaller than those of NC82 at the same time point. We observed 765 and 1,011 differentially expressed genes (DEGs) in Taiyan8 and NC82, respectively, in CMV-inoculated leaves. DEGs related to reactive oxygen species, salicylic acid signal transduction, and plant–pathogen interaction were upregulated or downregulated in Taiyan8, which indicates that defense response pathways to CMV were activated in the tolerant cultivar. In addition, we identified several DEGs related to disease defense and stress resistance showing opposing expression patterns in the two cultivars. Our comparative transcriptome analysis will improve our understanding of the mechanisms of CMV tolerance in plants, and will be of great importance in the molecular breeding of CMV- tolerant genotypes.

Phytophthora nicotianae is highly pathogenic to Solanaceous crops and is a major problem in tobacco production. The tobacco cultivar Beihart1000-1 (BH) is resistant, whereas the Xiaohuangjin 1025 (XHJ) cultivar is susceptible to infection. Here, BH and XHJ were used as models to identify resistant and susceptible genes using RNA sequencing (RNA-seq). Roots were sampled at 0, 6, 12, 24, and 60 h post infection. In total, 23,753 and 25,187 differentially expressed genes (DEGs) were identified in BH and XHJ, respectively. By mapping upregulated DEGs to the KEGG database, changes of the rich factor of “plant pathogen interaction pathway” were corresponded to the infection process. Of all the DEGs in this pathway, 38 were specifically regulated in BH. These genes included 11 disease-resistance proteins, 3 pathogenesis-related proteins, 4 RLP/RLKs, 2 CNGCs, 7 calcium-dependent protein kinases, 4 calcium-binding proteins, 1 mitogen-activated protein kinase kinase, 1 protein EDS1L, 2 WRKY transcription factors, 1 mannosyltransferase, and 1 calmodulin-like protein. By combining the analysis of reported susceptible (S) gene homologs and DEGs in XHJ, 9 S gene homologs were identified, which included 1 calmodulin-binding transcription activator, 1 cyclic nucleotide-gated ion channel, 1 protein trichome birefringence-like protein, 1 plant UBX domain-containing protein, 1 ADP-ribosylation factor GTPase-activating protein, 2 callose synthases, and 2 cellulose synthase A catalytic subunits. qRT-PCR was used to validate the RNA-seq data. The comprehensive transcriptome dataset described here, including candidate resistant and susceptible genes, will provide a valuable resource for breeding tobacco plants resistant to P. nicotianae infections.