Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)
Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)
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转录组分析揭示了参与棉花（Gossypium arboreum）纤维发育的长非编码RNA
DOI：
10.1007/s11427-016-5000-2
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发表时间：
2016-01
影响因子：
9.1
通讯作者：
Song Guoli
中科院分区：
文献类型：
--
作者：
Zou Changsong;Wang Qiaolian;Lu Cairui;Yang Wencui;Zhang Youping;Cheng Hailiang;Feng Xiaoxu;Mtawa Andrew Prosper;Song Guoli
长链非编码RNA（longnoncodingRNAs，lncRNA）在酵母、哺乳动物和植物的多种生物学调控过程中发挥重要作用。然而，在亚洲棉中还没有系统鉴定lncRNA的报道。本研究对棉花纤维和叶片样品进行了链特异性RNA测序（ssRNA-seq），系统地鉴定和分析了纤维起始和伸长过程中的lncRNA。我们鉴定了5，996个lncRNA，其中3，510个和2，486个可分别归类为长基因间非编码RNA（lincRNA）和天然反义转录物（lncNAT）。LincRNA和lncNAT在许多方面相似，但在外显子数目、外显子长度和转录物长度上存在一些差异。表达分析显示，51.9%的lincRNA和54.5%的lncNATs转录本在纤维发育的一个阶段优先表达，并且显著高于蛋白编码转录本（21.7%）。在纤维和快速伸长阶段，lncRNA的快速和动态变化可能有助于棉花纤维的发育。这项工作描述了一组参与纤维发育的lncRNA。lncRNA的特征和表达分析将有助于进一步研究其在棉花纤维发育中的作用。
Long noncoding RNAs (lncRNAs) play important roles in various biological regulatory processes in yeast, mammals, and plants. However, no systematic identification of lncRNAs has been reported inGossypium arboreum. In this study, the strand-specific RNA sequencing (ssRNA-seq) of samples from cotton fibers and leaves was performed, and lncRNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lncRNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs (lincRNAs) and natural antisense transcripts (lncNAT), respectively. LincRNAs and lncNATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of lincRNAs and 54.5% of lncNATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding transcripts (21.7%). During the fiber and rapid elongation stages, rapid and dynamic changes in lncRNAs may contribute to fiber development in cotton. This work describes a set of lncRNAs that are involved in fiber development. The characterization and expression analysis of lncRNAs will facilitate future studies on their roles in fiber development in cotton.
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