Identification and Validation of Potential Conserved microRNAs and Their Targets in Peach (Prunus persica)

Abstract

1MicroRNAs are a class of small, endogenous, non-coding RNA molecules that negatively regulate gene expression at the transcriptional or the post-transcriptional level. Although a large number of miRNAs have been identified in many plant species, especially from model plants and crops, they remain largely unknown in peach. In this study, 110 potential miRNAs belonging to 37 families were identified using computational methods. A total of 43 potential targets were found for 21 families based on near-perfect or perfect complementarity between the plant miRNA and the target sequences. A majority of the targets were transcription factors which play important roles in peach development. qRT-PCR analysis of RNA samples prepared from different peach tissues for 25 miRNA families revealed that miRNAs were differentially expressed in different tissues. Furthermore, two target genes were experimentally verified by detection of the miRNA-mediated mRNA cleavage sites in peach using RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE). Finally, we studied the expression pattern of the two target genes in three different tissues of peach to further understand the mechanism of the interaction between miRNAs and their target genes.

Integrative Analysis of miRNA and mRNA Profiles in Response to Ethylene in Rose Petals during Flower Opening

“…The length distribution of the small RNAs ranged from 18 to 30 nt was examined and shown in Figure 1. In all four samples, 21-nt, 23-nt and 24-nt small RNAs were the major population, consistent with the size of Dicer-like protein cleavage products, and 24-nt was the most dominant, similar to the results obtained from most tested plants, such as Arabidopsis thaliana , rice, tomato, cucumber, apple and peach [7], [9], [10], [11], [16], [17], [31], [32]. The redundancy level of sRNAs was low for the 23-nt and 24-nt sRNAs, while the 21-nt sRNAs have the highest redundancy level, especially in the E24 library.…”

“…Genome sequences of apple, peach and strawberry have been generated; however, research in small RNAs of the Rosaceae plant is still limited. Recently, miRNAs from apple and peach were reported [10], [11], [16], [17]. Unlike apple and peach which are important for their fresh fruits, rose is important for its beautiful and fragrant flowers.…”

Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach

“…Some of these differentially H3K27 trimethylated genes were considered as putative orthologs of Arabidopsis genes after reciprocal blast analysis. Many of these genes encode transcription factors harbouring MADS-box, MYB or NAC domains among others, and epigenetic regulators such as the microRNA ppe-miR172c (Gao et al 2012) and a putative histone acetyltransferase (ppb020787m).…”

Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

“…Recently, some groups have predicted or identified miRNAs and their target genes in peach. Zhang et al [29] and Gao et al [30] independently identified miRNAs by computational prediction and experimentally by verifying miRNAs via RT-qPCR and two miRNA target genes were validated using RLM-RACE. Several miRNAs responsive to drought [31] or chilling [32] and miRNAs in different tissues [28] were identified by high-throughput sequencing in peach.…”