Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
BMC Plant Biol. 2012 Aug 21;12:149. doi: 10.1186/1471-2229-12-149.
MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs.
We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach.
Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.
MicroRNAs (miRNAs) 最近被认为是植物中重要的基因调控因子。miRNAs 及其靶标在拟南芥和水稻中得到了广泛研究。然而，关于桃（Prunus persica）miRNAs 和其靶基因的特征，相对了解较少，桃是一种具有独特发育程序的复杂作物。
我们进行了小 RNA 深度测序，鉴定出 47 个桃特异性和 47 个已知 miRNA 或家族，它们具有不同的表达模式。鉴定出的 miRNA 共同靶向 80 个基因，其中许多以前没有报道过。与模式植物系统一样，桃具有三种保守的反式作用 siRNA 生物发生途径中的两种，具有相似的机制特征和靶标特异性。桃特有的是，三个 miRNA 共同靶向 49 个 MYBs，其中 19 个已知调节苯丙素代谢，这是一个与石硬化和果实颜色发育相关的关键途径，突出了 miRNA 在调节桃果实发育和成熟中的关键作用。我们还发现，大多数 miRNA 在不同组织中差异表达，部分原因是 miRNA 前体的差异加工。多达 16%的桃特异性 miRNA 以组织特异性的方式从前体中差异加工，这在植物细胞中很少观察到。miRNA 前体加工活性似乎与其转录活性无关，而是在桃中独立作用。
总之，这些数据描述了桃 miRNA 的独特表达模式和加工调控，并表明存在一个复杂的多层次 miRNA 调控网络，能够靶向多种生物学功能，包括苯丙素途径，其在桃果实发育中具有多方面的时空作用。
