Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa
Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa
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芜菁花粉发育和受精过程中长非编码RNA的系统鉴定
DOI：
10.1111/tpj.14016
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发表时间：
2018-10-01
期刊：
影响因子：
7.2
通讯作者：
Cao, Jiashu
中科院分区：
文献类型：
--
作者：
Huang, Li;Dong, Heng;Cao, Jiashu
长链非编码RNA（lncRNA）在植物发育中的重要性已被确立，但对花粉发育和受精过程中表达的lncRNA的系统分析还很困难。我们在芜菁花粉发育过程中的五个发育阶段和授粉后的三个不同时间点进行了时间序列的RNA-seq实验，鉴定了12051个推定的lncRNA。提供了支持花粉发育和受精的动态lncRNA表达网络的全面视图。B。rapa lncRNA具有lncRNA的许多共同特征：相对较短的长度，低表达但在狭窄的时间窗内特异性，以及低进化保守性。揭示了调控生殖发育如外壁形成的基因模块和关键lncRNA。47个顺式作用的lncRNA和451个反式作用的lncRNA被发现与它们的靶蛋白编码基因高度共表达。特别重要的是发现了14个lncRNA，它们与10个功能已知的花粉相关编码基因高度共表达。15个lncRNA被预测为13个miRNAs的内源性靶标模拟物，并且经过实验验证，两个lncRNA被证明是miR 160的功能性靶标模拟物，并且显示在花粉发育中起作用。我们的研究为B花粉发育和受精过程中lncRNA的系统鉴定提供了依据。并为未来的遗传、基因组和进化研究奠定了基础。
The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs expressed during pollen development and fertilization has been elusive. We performed a time series of RNA-seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12051 putative lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.