Solanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops. In this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique. Our work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied.

Ralstonia solanacearum is a soil and water-borne pathogen that can infect a wide range of plants and cause the devastating bacterial wilt disease. To successfully colonize a host, R. solanacearum requires the type III secretion system (T3SS), which delivers bacterial effector proteins inside the plant cells. HrpG is a central transcriptional regulator that drives the expression of the T3SS and other virulence determinants. hrpG transcription is highly induced upon plant cell contact and its product is also post-transcriptionally activated by metabolic signals present when bacteria are grown in minimal medium (MM). Here, we describe a transcriptional induction of hrpG at early stages of bacterial co-culture with plant cells that caused overexpression of the downstream T3SS effector genes. This induction was maintained in a strain devoid of prhA, the outer membrane receptor that senses bacterial contact with plant cells, demonstrating that this is a response to an unknown signal. Induction was unaffected after disruption of the known R. solanacearum pathogenicity regulators, indicating that it is controlled by a non-described system. Moreover, plant contact-independent signals are also important in planta, as shown by the hrpG induction triggered by apoplastic and xylem extracts. We also found that none of the amino acids or sugars present in the apoplast and xylem saps studied correlated with hrpG induction. This suggests that a small molecule or an environmental condition is responsible for the T3SS gene expression inside the plants. Our results also highlight the abundance and diversity of possible carbon, nitrogen and energy sources likely used by R. solanacearum during growth in planta.

Plants are often facing several stresses simultaneously. Understanding how they react and the way pathogens adapt to such combinational stresses is poorly documented. Here we developed an experimental system mimicking field intermittent drought on rice followed by inoculation by the pathogenic fungus Magnaporthe oryzae. This experimental system triggers an enhancement of susceptibility that could be correlated with the dampening of several aspects of plant immunity, namely the oxidative burst and the transcription of several pathogenesis-related genes. Quite strikingly, the analysis of fungal transcription by RNASeq analysis under drought reveals that the fungus is greatly modifying its virulence program: genes coding for small secreted proteins were massively repressed in droughted plants compared to unstressed ones whereas genes coding for enzymes involved in degradation of cell-wall were induced. We also show that drought can lead to the partial breakdown of several major resistance genes by affecting R plant gene and/or pathogen effector expression. We propose a model where a yet unknown plant signal can trigger a change in the virulence program of the pathogen to adapt to a plant host that was affected by drought prior to infection.