Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development.
Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development.
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小 RNA 分析和降解组分析揭示了 microRNA 在花生胚胎发生和早期豆荚发育中的调控
DOI：
10.1186/s12864-017-3587-8
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发表时间：
2017-03-02
期刊：
影响因子：
4.4
通讯作者：
Wang X
中科院分区：
文献类型：
--
作者：
Gao C;Wang P;Zhao S;Zhao C;Xia H;Hou L;Ju Z;Zhang Y;Li C;Wang X
作为一种典型的地下结实植物，花生的胚胎发生和荚果发育是复杂的过程，涉及许多基因调控途径，并受适宜的激素水平控制。微小RNA（miRNAs）是一类小的非编码RNA，在转录后基因调控中发挥着不可或缺的作用。最近，花生miRNAs的鉴定和特性描述已有报道。然而，miRNAs是否参与花生胚胎发生和荚果发育的调控仍有待探索。
在本研究中，构建了来自不同发育阶段花生早期荚果的小RNA和降解组文库并进行测序。共发现了70个已知的和24个新的miRNA家族。其中，16个miRNA家族是豆科植物特有的，12个家族是花生特有的。30个已知的和10个新的miRNA家族在荚果发育过程中差异表达。此外，通过降解组测序为47个miRNA家族鉴定了115个靶基因。发现了几个可能是花生特有的新靶标，并通过RNA连接酶介导的5′ cDNA末端快速扩增（RLM 5′ - RACE）进一步验证。此外，我们对几个靶基因的完整转录本和总转录本进行了分析，表明SPL（miR156/157）、NAC（miR164）、PPRP（miR167和miR1088）、AP2（miR172）和GRF（miR396）在早期荚果发育过程中分别受到积极调控。
通过深度测序鉴定出了大量的miRNAs及其相关靶基因。这些发现为花生荚果中miRNA介导的调控途径提供了新信息，这将有助于全面理解调控花生胚胎和早期荚果发育的分子机制。
本文的网络版（doi:10.1186/s12864 - 017 - 3587 - 8）包含补充材料，授权用户可获取。
BackgroundAs a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored.ResultsIn this study, small RNA and degradome libraries from peanut early pod of different developmental stages were constructed and sequenced. A total of 70 known and 24 novel miRNA families were discovered. Among them, 16 miRNA families were legume-specific and 12 families were peanut-specific. 30 known and 10 novel miRNA families were differentially expressed during pod development. In addition, 115 target genes were identified for 47 miRNA families by degradome sequencing. Several new targets that might be specific to peanut were found and further validated by RNA ligase-mediated rapid amplification of 5′ cDNA ends (RLM 5′-RACE). Furthermore, we performed profiling analysis of intact and total transcripts of several target genes, demonstrating thatSPL(miR156/157),NAC(miR164),PPRP(miR167 and miR1088),AP2(miR172) andGRF(miR396) are actively modulated during early pod development, respectively.ConclusionsLarge numbers of miRNAs and their related target genes were identified through deep sequencing. These findings provided new information on miRNA-mediated regulatory pathways in peanut pod, which will contribute to the comprehensive understanding of the molecular mechanisms that governing peanut embryo and early pod development.