Genome-Wide Identification of MicroRNAs That Are Responsive to Virus/Viroid Infection in Nectarine Trees Through High-Throughput Sequencing

Peach is one of the most widely grown fruit crops in China, nectarine [ Prunus persica (L.) Batsch var. nucipersica (Suckow) C.K. Schneid.] is an important commercial variety of peach. MicroRNAs (miRNAs) play important functions in post-transcriptional gene regulation in plants. In this study, miRNAs and their target genes were identified and predicted by sequencing four small RNA libraries prepared from nectarine leaf and fruit tissues infected with different virus/viroid combinations using next-generation sequencing technology (NGS). A total of 116 known peach miRNAs were identified, and 303 putative novel miRNAs were predicted. Some of these miRNAs were found to be highly conserved. Most of the novel miRNAs were 24-nt in length and many of these miRNAs came from MIR 5271 and MIR 7717 families. All differently expressed miRNAs had 2785 putative target genes. Comparative profiling revealed that 45 miRNAs exhibited significant differential expression between leaf and fruit tissue. Moreover, expression levels of these miRNAs were significantly affected in the two tissues despite the fact that the trees were infected by different virus/viroid combinations. We also found that there were more differentially expressed miRNAs in leaves tissue than in fruits, and a few miRNAs were identified that play important roles in the response to virus/viroid infection. Our results show that the expression of some miRNAs appears to be tissue-specific, and virus/viroid infection had a greater effect on the miRNA expression profiles in leaves than in fruits of nectarine. We hypothesize that virus/viroid infection induces the production of many novel miRNAs and also affects their lengths.