Discovering conserved insect microRNAs from expressed sequence tags

文献类型： 外文期刊

第一作者： Yu, Lun

作者： Yu, Lun;Li, Fei;Lin, Kejian;Liang, Jingdong

作者机构：

关键词： MicroRNA;Insect;EST;Computational identification;RT PCR

期刊名称：JOURNAL OF INSECT PHYSIOLOGY （ 影响因子：2.354； 五年影响因子：3.045 ）

ISSN： 0022-1910

年卷期： 2010 年 56 卷 12 期

页码：

收录情况： SCI

摘要： 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

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