ABSTRACT: Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Time-course RNAseq]
Project description:Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Strand-specific RNA-seq]
Project description:Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection
Project description:Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.
Project description:Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.
Project description:Importance: Pectobacterium species cause soft rot in potato and other host plants primarily by secreting a battery of plant cell wall degrading enzymes. In addition, several different secretion systems are mobilized during infection. Previous studies of gene expression and regulation thereof primarily focused on the onset of infection. This work investigated transcriptome changes in Pectobacterium during the infection of potato tubers up to 72 hours post inoculation to elucidate biological processes during a longer infection period. Methods: The transcriptomes of aggressive strains of the two species P. carotovorum subsp. carotovorum and P. polaris were investigated during infection of potato minitubers (cv. 'Asterix') at 24, 48 and 72 hours after inoculation by RNA sequencing. The transcriptomes were compared to that of bacteria grown on minimal M9 medium, and transcriptomes from later infection time points (48 and 72 hours after inoculation) were compared to early infection (24 hours after inoculation). Results: Plant cell wall degrading enzymes and secretion system associated genes were largely upregulated during infection compared to in vitro growth, but downregulated in the later phases of infection compared to the early infection phase. The downregulation was not sufficiently explained by the expression of known virulence regulators such as the RsmA/B or the ExpA/S systems.
Project description:Pectobacterium carotovorum subsp. brasiliense 1692 (Pcb1692) is an emerging pathogen of significance affecting potato production globally. In the current study, we reveal the complete transcriptome of Pcb in planta at the early and later stages of infection (24 and 72 hour post inoculation (hpi), respectively) using RNA-seq. We identified713 differentially expressed genes at 24hpi and an additional 157 differentially expressed genes at 72 hpi. Genes encoding PCWDEs and iron acquisition were up-regulated. The type VI secretion system (T6SS) and the bacteriocin (carotovoricin) gene clusters were both highly up-regulated, suggesting they might play a role in antibacterial activity in eliminating competition for nutrients with other microbes within the niche. Additionally, our results suggest the importance of genes involved in amino acid, carbohydrates, citrate metabolism, adhesion, chemotaxis, motility, metabolism as these were differentially expressed at 24 hpi. To establish the Pcb1692 quorum sensing regulon, the transcriptome of Pcb1692 wild-type compared to that of Pcb1692∆expI during in vitro growth and in planta at 24 hpi in potato tubers was analyzed. Important virulence factors such as T2SS, T6SS, and citrate metabolism were found to be under quorum sensing regulation while, carotovoricin did not appear to be quorum sensing dependent.
Project description:Transcription profiling of Nicotinan benthamiana in response to Pectobacterium carotovorum WPP14 and Pseudomonas syringae pv. tomato DC3000
