Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragariaxananassa)
Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragariaxananassa)
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DOI：
10.1111/j.1399-3054.2012.01713.x
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发表时间：
2013-07-01
影响因子：
6.4
通讯作者：
Fang, Jinggui
中科院分区：
文献类型：
--
作者：
Ge, Anjing;Shangguan, Lingfei;Fang, Jinggui
在植物中，microRNAs(MiRNAs)在转录后基因调控中起着关键作用，并已被证明控制着参与各种生物和代谢过程的许多基因。已有广泛的研究发现miRNAs并分析其在模式植物物种中的功能，如拟南芥和水稻。深度测序技术有助于识别植物中特定物种或低表达以及保守或高表达的miRNAs。本研究利用SolexA测序技术在栽培草莓(Fragariaxananassa)中发现了新的miRNAs。从从草莓果实组织中提取的小RNA生成的短RNA库中获得了23282个309个读数，代表22500个不同的序列。在序列相似性和发夹结构预测的基础上，我们发现代表153个序列的156639个阅读片段与已知的miRNAs有很好的匹配。我们还鉴定了37个新的miRNA候选基因。这些序列以前从未在其他植物物种中被描述过。预测了大多数和新的miRNAs的潜在靶基因。这些结果表明，在农业上重要的栽培草莓中存在调控miRNAs，并可能在其生长发育和对疾病的反应中发挥重要作用。
In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new miRNAs in cultivated strawberry (Fragariaxananassa). A total of 23282 309 reads representing 22500 402 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from strawberry fruit tissues. On the basis of sequence similarity and hairpin structure prediction, we found that 156639 reads representing 153 sequences have good matches to known miRNAs. We also identified 37 novel miRNA candidates. These sequences had not been previously described in other plant species. Potential target genes were predicted for the majority of and novel miRNAs. These results show that regulatory miRNAs exist in the agriculturally important cultivated strawberry and may play an important role in its growth, development and response to disease.