Integrated miRNA and mRNA expression profiling reveals the response regulators of a susceptible tomato cultivar to early blight disease

Abstract

Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host–pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated. Concomitantly, 5,450 mRNAs were significantly regulated in the same diseased tissues. Differentially expressed genes were most significantly associated with response to stimulus process, photosynthesis, biosynthesis of secondary metabolites, plant–pathogen interaction and plant hormone signal transduction pathways. GO term enrichment-based categorization of gene-functions further supported this observation, as terms related to pathogen perception, disease signal transduction, cellular metabolic processes including oxidoreductase and kinase activity were over represented. In addition, we have discovered 102 miRNA–mRNA pairs which were regulated antagonistically, and careful study of the targeted mRNAs depicted that multiple transcription factors, nucleotide-binding site leucine-rich repeats, receptor-like proteins and enzymes related to cellular ROS management were profoundly affected. These studies have identified key regulators of Alternaria-stress response in tomato and the subset of genes that are likely to be post-transcriptionally silenced during the infection.

Distinct transcriptional and processing regulations control miR167a level in tomato during stress

“…Tomato genome encodes about 30 miRNAs which are potentially derived from at least two alternative genes. 27 Among these, MIR167 precursors are likely expressed from five different genes. Previous literature 13 and our experimental evidences (Fig.…”

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

“…For instance, an extensive interaction analysis of mRNA and miRNA uncovered the molecular interactions between pathogen Potato virus Y and tobacco (Guo et al, 2017). Similarly, another study identified important regulators of Alternaria-stress response in tomato (Sarkar et al, 2017).…”

“…miRNAs control the expression of genes in spatial and temporal-specific manner in response to stress. A number of studies have suggested the importance of miRNAs in plant defense response (Kohli et al, 2014;Sarkar et al, 2017). Although miRNAs have been extensively studied in plants, their regulatory mechanism is still unclear on miRNA-mediated response to biotic stress.…”

“…Plant miRNAs are known to have perfect or near-perfect complementarity with their targets and can be predicted using both computational tools and sequencing approaches like degradome analysis. Recently, a few studies on the integrated analysis of mRNA and miRNA expression profiles have been published (Cao et al, 2017;Guo et al, 2017;Sarkar et al, 2017). For instance, an extensive interaction analysis of mRNA and miRNA uncovered the molecular interactions between pathogen Potato virus Y and tobacco (Guo et al, 2017).…”

miR‐197‐5p inhibits sarcomagenesis and induces cellular senescence via repression of KIAA0101

“…miRNAs are a class of small endogenous noncoding RNAs of about 18 to 25 nucleotides (nts), which are known to play diverse gene regulatory functions at the posttranscriptional level . They function by preferentially binding to the 3′‐untranslated region (3′‐UTR) of target mRNAs through their seed region (2‐7/8 nts) causing either degradation or translational inhibition of the corresponding target mRNAs .…”