Correlation of differentially expression miRNAs and mRNAs from 35S:SlmiR-168a and 35S:rSlAGO1 plants compared with WT plants
There is a regulatory relationship between miRNAs and mRNAs, and this relationship can be established through target gene prediction. In this study, we found 113 miRNA/mRNA pairs in the comparison of35S:SlmiR-168a and WT plants, with both positive and negative correlations (Table S10), and 93 miRNA/mRNA pairs in the comparison of35S:rSlAGO1 and WT plants, with both positive and negative correlations (Table S11). Owing to various regulatory factors, the expression of mRNAs by miRNAs did not have a completely inverse relationship, and both positive and negative correlations were detected. For most cases involving target cleavage, the simple expectation is that when miRNAs are induced, the expression levels of their target mRNAs are reduced and vice versa. There were 74 negative miRNA/mRNA interactions in the comparison of 35S:SlmiR-168a with WT (Table S10) and 49 negative miRNA/mRNA interactions in the comparison of 35S:rSlAGO1with WT (Table S11). Although AGO1 is known to be important for the stabilisation of miRNAs, its role in miRNA production has not been established (Vaucheret et al. 2004). However, our findings identified 10 upregulated miRNA and downregulated mRNA interaction pairs in the comparison of 35S:rSlAGO1 with WT and two downregulated miRNA and upregulated mRNA interaction pairs in the comparison of35S:SlmiR-168a with WT (Table 1). Thus, these miRNAs were thought to be stabilised by AGO1 protein. GO analysis of the 12 negative miRNA/mRNA pairs identified 28 functional processes that involved the CTK-activated signalling pathway, responses to salt stress, and responses to ABA (Figs. S1 and S3). Additionally, pathway enrichment analysis of the 12 negative miRNA/mRNA pairs identified four pathways, including plant/pathogen interactions, plant hormone signal transduction, base excision repair, and histidine metabolism (Fig. S2).