ABSTRACT
Ralstonia solanacearum, a bacterial plant pathogen, poses a significant threat to tomato (Solanum lycopersicum) production through destructive wilt disease. While noncoding RNA has emerged as a crucial regulator in plant disease, its specific involvement in tomato bacterial wilt remains limited. Here, we conducted a comprehensive analysis of the transcriptional landscape, encompassing both mRNAs and noncoding RNAs, in a tomato resistant line ('ZRS_7') and a susceptible line ('HTY_9') upon R. solanacearum inoculation using high-throughput RNA sequencing. Differential expression (DE) analysis revealed significant alterations in 7506 mRNAs, 997 lncRNAs, and 69 miRNAs between 'ZRS_7' and 'HTY_9' after pathogen exposure. Notably, 4548 mRNAs, 367 lncRNAs, and 26 miRNAs exhibited genotype-specific responses to R. solanacearum inoculation. GO and KEGG pathway analyses unveiled the potential involvement of noncoding RNAs in the response to bacterial wilt disease, targeting receptor-like kinases, cell wall-related genes, glutamate decarboxylases, and other key pathways. Furthermore, we constructed a comprehensive competing endogenous RNA (ceRNA) network incorporating 13 DE-miRNAs, 30 DE-lncRNAs, and 127 DEGs, providing insights into their potential contributions to the response against bacterial inoculation. Importantly, the characterization of possible endogenous target mimics (eTMs) of Sly-miR482e-3p via VIGS technology demonstrated the significant impact of eTM482e-3p-1 silencing on tomato's sensitivity to R. solanacearum. These findings support the existence of an eTM482e-3p-1-Sly-miR482e-3p-NBS-LRRs network in regulating tomato's response to the pathogen. Collectively, our findings shed light on the intricate interactions among lncRNAs, miRNAs, and mRNAs as underlying factors in conferring resistance to R. solanacearum in tomato.
Subject(s)
MicroRNAs , RNA, Long Noncoding , Ralstonia solanacearum , Solanum lycopersicum , Ralstonia solanacearum/genetics , Ralstonia solanacearum/metabolism , Solanum lycopersicum/genetics , Transcriptome , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Plant Diseases/genetics , Plant Diseases/microbiologyABSTRACT
An increasing number of non-coding RNAs (ncRNAs) have been discovered recently with the advance of RNA-seq. Nevertheless, the function of ncRNAs in leaf senescence was not fully elucidated. In this study, the whole transcriptome sequencing was employed to characterize the expression profiles of mRNA, lncRNA and miRNA during leaf senescence. A total of 2774 mRNAs, 160 lncRNAs and 117 miRNAs were identified to be significantly differentially expressed between the senescent and the young leaves. Co-expression analysis showed that 160 differential expressing (DE) lncRNAs potentially regulated 946 protein-coding genes in trans, but only 32 targeted protein-coding genes were predicated to be regulated by 30 lncRNAs in cis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of these trans- and cis-target genes revealed that the DE lncRNAs participated in pathways, such as photosynthesis, transporters and circadian rhythm. Furthermore, virus-induced gene silencing (VIGS) was employed to illuminate the role of lncRNAs. The silence of MSTRG.16920 and MSTRG.7613, two intergenic lncRNAs, significantly inhibited leaf senescence induced by darkness, presumably attributed to the downregulated expression of their corresponding target genes Solyc02g069960 and Solyc06g050440, respectively. Notably, Solyc02g069960 and Solyc06g050440 encoding senescence-related NAC transcription factor and reactive oxygen species (ROS)-related peroxidase, respectively, served as positive regulators of leaf senescence. Collectively, our study provides a comprehensive expression profile of lncRNAs in senescent leaf with the concurrent integrated expression of mRNAs and miRNAs.
