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

Xiaoyan Luo,Ting Shi,Zhen Zhang,Zhaojun Ni,Zongming Cheng,Zhihong Gao,Zhanjiang Liu

doi:10.1371/journal.pone.0079090

Xiaoyan Luo, Ting Shi + Show 5 more

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https://doi.org/10.1371/journal.pone.0079090

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Journal: PloS one	Publication Date: Nov 13, 2013
Citations: 34	License type: CC BY 4.0

Affiliation: Nanjing Agricultural University

Abstract

MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.

Highlights

MicroRNAs are small, endogenous, non-coding small RNAs that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts [1,2]
The pre-miRNA is further cleaved to a miRNA duplex and one of the strands of this duplex is incorporated into the RNA-induced silencing complex (RISC) [8]
Small RNA Sequencing Analysis To identify miRNAs involved in tissue development, a small

Summary

Introduction

MicroRNAs (miRNAs) are small, endogenous, non-coding small RNAs that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts [1,2]. Plant miRNAs are transcribed by RNA polymerase II to generate primary miRNA (pri-miRNA) transcripts and cleaved to miRNA precursors (pre-miRNAs), catalysed by a Dicer-like enzyme (DCL1) [6,7]. The pre-miRNA is further cleaved to a miRNA duplex (miRNA:miRNA*) and one of the strands of this duplex is incorporated into the RNA-induced silencing complex (RISC) [8]. The miRNA* strand is usually degraded, in some cases it accumulates at a lower level [9]. The mature miRNA strand guides ARGONAUTE (AGO) to complementary target mRNA resulting in silencing of the target gene [10,11]

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