Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach.Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.There are many mechanisms by which plants regulate gene expression to ensure normal development and appropriate responses to both biotic and abiotic signals. One regulatory mechanism involves endogenous small RNA (sRNA) molecules, 20~24-nt in length [1,2], which act by silencing gene expression. In plants, sRNAs have been classified based on their biogenesis, including microRNAs (miRNAs), heterochromatic siRNAs (hc-siRNAs), trans-acting siRNAs (tasiRNAs) and natur