Discovering conserved insect microRNAs from expressed sequence tags
Discovering conserved insect microRNAs from expressed sequence tags
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从表达的序列标签中发现保守的昆虫 microRNA。
DOI：
10.1016/j.jinsphys.2010.07.007
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发表时间：
2010-12-01
影响因子：
2.2
通讯作者：
Li, Fei
中科院分区：
文献类型：
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作者：
Jia, Qidong;Lin, Kejian;Li, Fei
microRNA（miRNA）在动物体内通过翻译抑制参与多种生物学途径的调控，近年来受到越来越多的关注。然而，对农业上重要害虫的miRNA基因的研究却很少。首先收集了63种昆虫的980 697条EST序列，并用于检索nr数据库。编码ESTs接下来使用已知的成熟miRNA与非编码ESTs进行比对。将含有成熟miRNA序列的ESTs作为候选ESTs。SVM算法结果，根据严格的标准，从30种昆虫中发现了86个miRNAs，而根据宽松的标准，从51种昆虫中发现了330个miRNAs。进化分析表明，mir-467、mir-297和mir-297是miRNAs的主要来源。466个是昆虫中最保守的miRNAs家族。为了证实推测的昆虫miRNAs的可靠性，我们研究了9个预测的miRNAs在飞蝗中的表达谱。大多数miRNAs在所有检测的组织和发育阶段都普遍表达，而Lmi-mir-509在2、4、5龄和成虫的胸部特异性表达。我们的所有工作报告了一种有效的计算策略，用于从昆虫EST中预测miRNAs基因，并在不同的昆虫物种中提出了数十种miRNAs，这些miRNAs有望参与许多重要的生理过程（C）。2010爱思唯尔有限公司版权所有
MicroRNAs (miRNA) participate in regulating diverse biological pathways by translational repression in animals They have attracted increasing attention recently However little work has been done on the miRNA genes in agriculturally important pests Because the transcripts of most miRNA genes are the products of type-II RNA polymerase pri-miRNA has a poly(A) tail and appears in expressed sequence tags (EST) We developed a computational pipeline to identify miRNA genes from insect ESTs First 980 697 ESTs from 63 Insects were collected and used to search the nr database The ESTs which did not share significant similarities with any known protein-coding genes were treated as non-coding ESTs Next known mature miRNAs were used to align with non-coding ESTs The ESTs which contain the sequence of mature miRNA were treated as candidate ESTs Finally putative precursors were extracted flanking the mature miRNA region in candidate ESTs and evaluated by the Triplet-SVM algorithm As a result 86 miRNAs from 30 Insect species were found based on a strict criterion while 330 miRNAs from 51 species were found based on a loose criterion Evolution analysis indicated that mir-467 mir-297 and mir-466 were the highest conserved miRNA families in insects To confirm the reliability of putative insect miRNAs the expression profile of nine predicted miRNAs in Locusta migratoria was investigated Eight miRNAs were successfully detected by RT-PCR. Most miRNAs were expressed ubiquitously at all examined tissues and developmental stages whereas Lmi-mir-509 was specifically expressed in the thorax of the 2nd 4th and 5th instars and adult locust In all our work reported an efficient computational strategy for predicting miRNA genes from insect ESTs and presented tens of miRNAs in diverse insect species which are expected to participate in many important physiological processes (C) 2010 Elsevier Ltd All rights reserved