Transcriptomic profiling of dynamic alternative splicing during the early response to Ralstonia solanacearum infection in tobacco roots

The pathogenic bacterium, Ralstonia solanacearum, causes bacterial wilt disease in many crops, which leads to significant yield losses worldwide. Although genes associated with resistance to this pathogen have been isolated and characterized in crops, the molecular mechanisms underlying the plant–pathogen interactions remain to be elucidated. Here, we performed a comparative transcriptional profiling analysis of tobacco (Nicotiana tabacum) cultivars C048 (susceptible) and C244 (resistant) in response to R. solanacearum infection. We found that the number of down- and up-regulated genes increased dramatically 3 h post inoculation (hpi), peaked 24 hpi, and then decreased 48 and 72 hpi, representing a “transcriptomic shock”. Of these genes, those associated with biotic and abiotic stresses and secondary metabolism were up-regulated, whereas those associated with primary metabolism were down-regulated. Alternative splicing (AS) modulates root defense against R. solanacearum by fine-tuning gene expression during the transcriptomic responses to pathogen invasion. The numbers of skipped exon (SE) and mutually exclusive exon (MXE) type AS events were reduced by approximately 60–80% in roots 9–72 hpi compared to those occurring 0–3 hpi. On the contrary, the number of differential alternative splicing (DAS) events showing a change in isoform ratio between samples increased, and most of them were associated with the down-regulation of corresponding gene expression. In addition, genes encoding transcription factors and leucine-rich repeat domain proteins that showed changes in both expression level and AS profile during pathogen infection were identified. Our study offers novel insights into the mechanisms underlying the transcriptional and post-transcriptional regulation of the tobacco response to R. solanacearum infection and will benefit the molecular breeding of pathogen-resistant tobacco in the future.