Transcriptomic analysis of ncRNA and mRNA interactions during leaf senescence in tomato

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.