Identification of microRNAs and transcript targets in Jatropha seeds. Jatropha curcas

MicroRNAs or miRNAs are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received much attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library from mature seeds and three mRNA libraries, from three different stages of seed development, were generated by deep sequencing in order to identify and characterize miRNAs and pre-miRNAs of J. curcas. Computation analysis allowed the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs), as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense and also lipid metabolism. Some of pre-miRNA and miRNA targets have different abundance among the three stages of seed development. A search for sequences that produce siRNA was performed indicating that J. curcas siRNAs play a role in nuclear functions, transport, catalytic process and diseases resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing and contributes to understand the function of these miRNAs. Overall design: microRNA identification in a mature seed library of Jatropha curcas by deep sequencing (Illumina HiSeq2000).

微小核糖核酸（microRNAs, miRNAs）是一类内源编码的小RNA，在多种植物生物学过程中发挥关键调控作用。麻疯树（Jatropha curcas L.）作为可生产可再生油料的潜在油料作物，受到学界广泛关注。
本研究通过深度测序技术构建了麻疯树成熟种子的小RNA（small RNA, sRNA）文库，以及取自种子发育三个不同阶段的3个信使RNA（messenger RNA, mRNA）文库，旨在鉴定并解析麻疯树的miRNAs及其前体（pre-miRNAs）。
通过生物信息学分析，本研究共鉴定到180个保守型miRNAs与41个pre-miRNAs，同时发现16个新型pre-miRNAs。预测得到的miRNA靶基因参与了广泛的生理过程，涵盖细胞结构构建、细胞核功能调控、翻译过程、物质转运、激素合成、免疫防御以及脂质代谢等多个方面。
部分pre-miRNA及其对应的miRNA靶基因在种子发育的三个阶段中呈现出差异化的表达丰度。
本研究针对产生小干扰RNA（small interfering RNA, siRNA）的序列开展了检索分析，结果显示麻疯树siRNA参与了细胞核功能调控、物质转运、催化反应以及病害抗性调控等生理活动。
本研究首次基于深度测序技术，在麻疯树成熟种子中实现了大规模miRNAs及其靶基因的鉴定，为解析这类miRNAs的生物学功能提供了重要研究基础。
实验设计：通过深度测序（Illumina HiSeq2000）对麻疯树成熟种子文库进行miRNA鉴定。