Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing.
Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing.
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DOI：
10.1186/1471-2229-12-218
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发表时间：
2012-11-19
影响因子：
5.3
通讯作者：
Mun JH
中科院分区：
文献类型：
--
作者：
Kim B;Yu HJ;Park SG;Shin JY;Oh M;Kim N;Mun JH
MicroRNA（miRNA）是参与植物基因组表观遗传控制的功能性非编码小RNA之一。尽管植物的基因组中同时含有进化保守的 miRNA 和物种特异性 miRNA，但计算方法通常只能识别进化保守的 miRNA。最近对甘蓝基因组的测序使我们能够识别 miRNA 及其假定的靶基因。在本研究中，我们试图基于高通量小 RNA 深度测序提供更全面的白菜 miRNA 预测。我们对五种组织的小 RNA 进行了测序：幼苗、根、叶柄、叶子和花。通过分析映射到白菜基因组的 275 万个独特读数，我们鉴定了 216 个新的 miRNA 和 196 个保守的 miRNA，预计它们会靶向基因组中约 20% 的蛋白质编码基因。对五种组织中 miRNA 的定量分析表明，新型 miRNA 在不同组织中表达，但其表达水平低于保守 miRNA。对白菜和拟南芥基因组之间 miRNA 的比较分析表明，白菜基因组中保守 miRNA 的冗余拷贝可能在全基因组三倍体后被删除。新的 miRNA 成员似乎是从白菜和拟南芥基因组中自发产生的，这表明 miRNA 的物种特异性扩展。我们已在名为 BraMRs 的白菜 miRNA 数据库中公开提供这些数据。该数据库允许用户从此处研究的五种组织类型中检索 miRNA 序列、其表达谱以及其靶基因的描述。这是第一份利用全基因组高通量技术从芸苔属作物中鉴定新型 miRNA 的报告。计算方法和小 RNA 深度测序相结合，可以对基因组中的 miRNA 进行可靠的预测。许多新的 miRNA 的发现，其中许多靶基因很少且表达水平较低，表明 miRNA 基因的快速进化。 miRNA数据库BraMRs的开发使我们能够整合miRNA识别、靶点预测和靶基因的功能注释。 BraMR 将成为一种宝贵的公共资源，可用于研究白菜和其他密切相关的芸苔属物种的表观遗传控制。该数据库可通过以下链接获取：http://bramrs.rna.kr [1]。
MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing. We sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the B. rapa genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome’s protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here. This is the first report to identify novel miRNAs from Brassica crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].
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影响因子：
7
作者：
Blanc, G;Hokamp, K;Wolfe, KH
通讯作者：
Wolfe, KH
影响因子：
14.9
作者：
Dai X;Zhao PX
通讯作者：
Zhao PX
影响因子：
14.9
作者：
Kozomara A;Griffiths-Jones S
通讯作者：
Griffiths-Jones S
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P