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).