Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean.
Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean.
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通过高通量测序对大豆中的环状 RNA 进行全基因组鉴定和表征
DOI：
10.1038/s41598-017-05922-9
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发表时间：
2017-07-17
影响因子：
4.6
通讯作者：
Jiao Y
中科院分区：
文献类型：
--
作者：
Zhao W;Cheng Y;Zhang C;You Q;Shen X;Guo W;Jiao Y
环状RNA（circRNA）在前体mRNA剪接过程中产生，其中3′和5′端通过共价键彼此连接。大豆是一个古老的四倍体，它经历了两次全基因组复制。大豆基因大多数是多拷贝的旁系同源基因。尽管在动物和植物中已经鉴定了许多circRNA，但对大豆circRNA，特别是来自旁系同源基因的circRNA知之甚少。在这里，我们使用深度测序技术结合RNase R富集策略和生物信息学方法来揭示大豆中的circRNA。总共鉴定了5，372个circRNA，其中约80%是由旁系同源基因产生的旁系同源circRNA。尽管具有高度的序列同源性，但旁系同源基因可以产生具有不同表达模式的不同旁系同源circRNA。2134个circRNA被预测为92个miRNAs靶标模拟物。CircRNA及其亚型在大豆中表现出组织特异性表达。基于circRNA-宿主基因的功能，大豆circRNA可能参与许多生物学过程，如发育过程、多生物过程和代谢过程。本研究不仅为大豆中circRNA的功能研究提供了基础，也为植物circRNA王国的研究提供了新的视角。
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3′ and 5′ ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.
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影响因子：
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作者：
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DOI：
10.1261/rna.052282.115
发表时间：
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期刊：
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影响因子：
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作者：
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