Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis.
Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis.
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通过高通量测序和生物信息学分析鉴定条斑紫菜 miRNA。
DOI：
10.1371/journal.pone.0010698
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发表时间：
2010-05-19
期刊：
影响因子：
3.7
通讯作者：
Ye N
中科院分区：
文献类型：
--
作者：
Liang C;Zhang X;Zou J;Xu D;Su F;Ye N
miRNA是一类长度约为22个核苷酸的非编码小RNA，通过直接结合或切割靶mRNA在基因表达的翻译水平调控中发挥重要作用。条斑紫菜（Porphyrayezoensis）是世界上最重要的海洋经济作物之一。到目前为止，仅在绿色单胞藻中发现了少量的miRNAs，还没有关于紫菜miRNAs的报道。为了鉴定条斑紫菜中的miRNAs，构建了条斑紫菜小RNA文库。使用Solexa技术进行文库的高通量测序和随后的生物信息学分析以鉴定新的miRNA。具体而言，180，557，942个读段产生了13，324个独特的miRNA，代表了在其他植物物种中鉴定的224个保守的miRNA家族。此外，从有限数量的EST中预测了7种新的推定miRNA。基于序列同源性搜索，预测了这些miRNAs的潜在靶点。这项研究提供了第一个大规模克隆和表征紫菜miRNAs及其潜在的目标。这些miRNAs属于224个保守的miRNAs家族，其中7个miRNAs是紫菜中的新发现。这些miRNAs为不断增长的新miRNAs数据库增添了新的内容，为进一步了解miRNAs在条斑紫菜发育调控中的功能奠定了基础。
miRNAs are a class of non-coding, small RNAs that are approximately 22 nucleotides long and play important roles in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. The red alga, Porphyra yezoensis is one of the most important marine economic crops worldwide. To date, only a few miRNAs have been identified in green unicellar alga and there is no report about Porphyra miRNAs. To identify miRNAs in Porphyra yezoensis, a small RNA library was constructed. Solexa technology was used to perform high throughput sequencing of the library and subsequent bioinformatics analysis to identify novel miRNAs. Specifically, 180,557,942 reads produced 13,324 unique miRNAs representing 224 conserved miRNA families that have been identified in other plants species. In addition, seven novel putative miRNAs were predicted from a limited number of ESTs. The potential targets of these putative miRNAs were also predicted based on sequence homology search. This study provides a first large scale cloning and characterization of Porphyra miRNAs and their potential targets. These miRNAs belong to 224 conserved miRNA families and 7 miRNAs are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development.
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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
DOI：
10.1073/pnas.0908718106
发表时间：
2009-12-29
影响因子：
11.1
作者：
Nag, Anwesha;King, Stacey;Jack, Thomas
通讯作者：
Jack, Thomas
影响因子：
7.4
作者：
Mette, MF;van der Winden, J;Matzke, AJM
通讯作者：
Matzke, AJM
影响因子：
3.3
作者：
Floyd, Sandra K.;Zalewski, Christopher S.;Bowman, John L.
通讯作者：
Bowman, John L.
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.