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首页> 外文期刊>Journal of Experimental Botany >Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing
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Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

机译：通过深度测序在鹰嘴豆中保守和新颖的微小RNA的全基因组发现和差异调控

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摘要

MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct small RNA sequences. We identified a total of 440 conserved miRNAs in chickpea based on sequence similarity with known miRNAs in other plants. In addition, 178 novel miRNAs were identified using a miRDeep pipeline with plant-specific scoring. Some of the conserved and novel miRNAs with significant sequence similarity were grouped into families. The chickpea miRNAs targeted a wide range of mRNAs involved in diverse cellular processes, including transcriptional regulation (transcription factors), protein modification and turnover, signal transduction, and metabolism. Our analysis revealed several miRNAs with differential spatial expression. Many of the chickpea miRNAs were expressed in a tissue-specific manner. The conserved and differential expression of members of the same miRNA family in different tissues was also observed. Some of the same family members were predicted to target different chickpea mRNAs, which suggested the specificity and complexity of miRNA-mediated developmental regulation. This study, for the first time, reveals a comprehensive set of conserved and novel miRNAs along with their expression patterns and putative targets in chickpea, and provides a framework for understanding regulation of developmental processes in legumes.
机译：MicroRNA（miRNA）是协调植物发育的复杂基因调控网络的重要组成部分。尽管已经为豆科植物鹰嘴豆开发了几种基因组资源，但迄今为止尚未发现miRNA。为了在鹰嘴豆（Cicer arietinum）中发现全基因组的miRNA，我们使用Illumina技术对来自七个主要组织/器官的小RNA含量进行了测序。产生了约1.54亿次读取，代表超过2000万个不同的小RNA序列。基于与其他植物中已知miRNA的序列相似性，我们在鹰嘴豆中鉴定出总共440个保守miRNA。此外，使用具有植物特异性评分的miRDeep途径鉴定了178种新颖的miRNA。一些具有显着序列相似性的保守的和新颖的miRNA被分为家族。鹰嘴豆miRNA靶向多种涉及多种细胞过程的mRNA，包括转录调控（转录因子），蛋白质修饰和更新，信号转导和代谢。我们的分析揭示了几种具有差异空间表达的miRNA。许多鹰嘴豆miRNA以组织特异性方式表达。还观察到相同miRNA家族成员在不同组织中的保守表达和差异表达。某些相同的家庭成员预计会针对不同的鹰嘴豆mRNA，这表明miRNA介导的发育调控的特异性和复杂性。这项研究首次揭示了一套完整的保守和新颖的miRNA及其在鹰嘴豆中的表达模式和推定的靶标，并为理解豆类发育过程的调控提供了框架。

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