Prunus persica Raw sequence reads. Prunus persica

Peach is an important drupe fruit tree which fruit is displaying a typical double sigmoidal growth curve. MicroRNAs (miRNAs) have been proved play vital roles in the regulation of fruit development. Although some miRNAs has been identified in peach fruit by different methods, but there remains a dearth of comprehensive data on the characterization of miRNAs and their target genes during three key develop phases of its fruit double sigmoidal growth curve. In this study, by high-throughput sequencing of small RNAs, 116 known miRNAs belonging to 70 families and 94 novel miRNAs were identified in days post-anthesis 20 (DPA20), DPA75 and DPA90 libraries, which represent initial period of exponential growth(FWI), period of slow growth(FWII) and second period of exponential growth(FWIII), respectively. Among them, 97 and 79 miRNAs were shown to be differentially expressed in DPA50 vs DPA20 and DPA75 vs DPA50 libraries. Meanwhile, 216 targets were identified for 68 known and 14 novel miRNAs in three libraries using degradome sequencing. Moreover, the expression patterns of 4 miRNAs and their targets were examined by qRT-PCR during fruit development and ripening. Finally, integrative analysis of miRNAs, their targets and GO terms revealed a complex miRNA-mRNA regulatory network involving a wide variety of biological processes, which mainly in auxin signaling pathway and that responsible for fruit enlargement. Our findings confirmed the importance of Ppe-miRNAs in peach fruit development and these will facilitate future investigations of the miRNA-mediated mechanisms that regulate fruit development in drupe fruit trees.