Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
PLoS One. 2013 Jul 24;8(7):e69995. doi: 10.1371/journal.pone.0069995. Print 2013.
MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean.
Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed.
The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae.
MicroRNAs (miRNAs) 是内源性编码的小 RNA，它们在后转录水平上调控基因表达，在许多发育和生理过程中发挥着重要作用。目前，关于模式非食用油料作物蓖麻（Ricinus communis L.）的转录组和组织特异性 miRNA 表达的信息很少，蓖麻是世界上最重要的非食用油料作物之一。测序技术的最新进展使得在许多植物物种中鉴定出了保守和新的 miRNA。在这里，我们使用高通量测序技术来鉴定和描述蓖麻中的 miRNA。
从蓖麻的根尖、叶片、发育中的种子（初始阶段种子 1；快速油脂积累阶段种子 2）和胚乳中构建了 5 个小 RNA 文库进行深度测序。高通量测序在本研究中产生了大量的小 RNA 序列。总共鉴定出 86 个保守 miRNA，包括 63 个已知的和 23 个新的。在蓖麻的保守 miRNA 中发现了 16 个 miRNA 同型变体。miRNA 在五个文库中的表达水平表现出不同的组织特异性。结合 miRNA 注释标准和 RT-PCR 方法，注释了 72 个新的 miRNA 和它们的潜在前体，并验证了 20 个新鉴定的 miRNA。此外，还提出了本研究中新鉴定 miRNA 的新靶候选物。
本研究首次在蓖麻中进行了高通量小 RNA 测序研究，以鉴定其 miRNA 群体。它描述并增加了在蓖麻中鉴定的 miRNA 及其同型的数量。miRNA 表达分析为理解蓖麻 miRNA 组织特异性表达模式提供了基础。本研究为蓖麻和大戟科其他成员提供了一个扩展的 miRNA 图谱。
