Function analysis of miRNA predicted targets
Putative targets for 107 differentially expressed miRNAs were identified (Table S8), and the identified target genes are listed in Table S9. Gene ontology (GO) enrichment analysis for the predicted targets of the 107 miRNAs identified 20 terms, including nucleus, plasma membrane, and ATP binding, that changed significantly (P < 0.00015) between the two transgenic tomato plants compared with those in the WT plants (Fig. 6a). Pathway enrichment analysis for the predicted targets of the 107 miRNAs identified 20 pathways, including ABC transporters, glycerophospholipid metabolism, circadian rhythem-plant, and RNA degradation, that changed significantly (P < 0.05) between the two transgenic tomato plants compared with those in the WT plants (Fig. 6b).