Title: Identification of peach (Prunus persica) miRNAs and their targets by deep sequencing and degradome analysis Authors
Submitted to: Biomed Central (BMC) Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 13, 2012
Publication Date: August 21, 2012
Citation: Zhu, H., Xia, R., Dardick, C.D., Callahan, A.M., An, Y., Liu, Z. 2012. Identification of peach (Prunus persica) miRNAs and their targets by deep sequencing and degradome analysis. Biomed Central (BMC) Plant Biology. DOI:10.1186/1471-2229-12-149. Interpretive Summary: Peach is one of the important horticultural crops and the fruit quality and productivity as well as resistance to pathogens and insects are determined by specific genes and regulatory networks that are rarely understood now. Small RNA-mediated gene regulation and networks have been recently illustrated, to some degree, in model and agronomically important crops. In this work, we took advantage of the power of current genomic tools and identify and characterize several groups of the miRNAs in peach plants. We have successfully identified 30 novel miRNAs as well as 47 conserved miRNAs. We also showed these miRNAs express in various peach tissues. This is our first step to fully unravel small RNA-mediated gene regulation and their relevance to fruit development, quality and storage as well as to resistance to various pathogens and insects in the long term.
Technical Abstract: MicroRNAs (miRNAs) are endogenous single-stranded small RNA molecules (sRNA) that are fundamental post-transcriptional regulators of gene expression. Many conserved plant miRNAs play important roles in plant growth and development, but more species-specific miRNAs remain to be identified and characterized. In this study, we combined next-generation sequencing (NGS), bioinformatic and molecular methods to identify conserved and peach-specific miRNAs in four peach (Prunus persica) tissues. A total of 23 conserved and 24 other known miRNA families were recovered in all four RNA libraries. Additionally, we identified 30 novel peach miRNAs with their star strands; most derived from single genes. Eighteen other putative miRNA candidates were also described. We confirmed 52 percent of the identified peach-specific miRNAs by northern blot analysis. Most conserved and novel miRNAs identified from peach showed tissue-specific expression, which was also observed for many of their precursor transcripts. The deep sequencing of a degradome library of mixed peach tissues identified 75 target mRNAs of known miRNAs; other 20 target mRNAs were also described for peach-specific miRNAs. We identified two trans-acting gene loci from the peach genome (PpeTAS3/4), generating the miRNA-directed 21-nt phasing pattern. We found two peach ARF homologs as targets for TAS3-siRNA that are cleaved by miR390, but no target was identified for TAS4-siRNA from miR828-directed cleavage.