茄子microRNAs与其靶基因的生物信息学预测

doi:10.3724/SP.J.1005.2011.00776

遗传 ›› 2011, Vol. 33 ›› Issue (7): 776-784.doi: 10.3724/SP.J.1005.2011.00776

茄子microRNAs与其靶基因的生物信息学预测

张磊^1,2, 晁江涛¹, 崔萌萌¹, 陈雅琼^1,2, 宗鹏^1,2, 孙玉合¹

1. 中国农业科学院烟草研究所, 中国农业科学院烟草遗传改良与生物技术重点开放实验室, 青岛 266101 2. 中国农业科学院研究生院, 北京 100081

收稿日期:2011-03-27 修回日期:2011-04-27 出版日期:2011-07-20 发布日期:2011-07-25
通讯作者: 孙玉合 E-mail:yhsun@163.com
基金资助:
国家烟草专卖局重点科技项目(编号：110200701021)资助

Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)

ZHANG Lei^1,2, CHAO Jiang-Tao¹, CUI Meng-Meng¹, CHEN Ya-Qiong^1,2, ZONG Peng^1,2, SUN Yu-He¹

1. Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Chinese Academy of Agricultural Sciences, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China 2. Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China

Received:2011-03-27 Revised:2011-04-27 Online:2011-07-20 Published:2011-07-25

摘要/Abstract

摘要： microRNAs(miRNAs)是一类在真核生物中发现的长度为21 nt左右、非编码、内源性的单链小分子RNA, 通过与靶基因的互补发挥转录后水平的负调控作用。目前, 已在许多物种中报道了miRNAs的存在, 然而还未见关于茄子miRNAs的报道。根据miRNAs在植物中的高度保守性及其前体的二级结构特征, 文章通过同源预测的方法, 将已知植物的miRNAs与茄子EST数据库比对, 经过一系列的筛选, 最终预测到12个家族的16条茄子miRNAs, 其中包括3个miRNA家族的正义/反义miRNAs, 而miR390和miR399家族的正义/反义miRNAs属于第一次发现。文章还通过在线软件psRNATarget预测到15条茄子miRNAs的71个靶基因, 这些靶基因主要编码与茄子生长发育、新陈代谢以及胁迫响应等过程相关的蛋白。

关键词: microRNAs(miRNAs), 靶基因, 生物信息学, EST, 茄子

Abstract: MicroRNAs (miRNAs), a recently discovered class of small (~21nt), non-coding, endogenous, single-stranded RNAs in eukaryotes, regulate gene expression negatively at the post-transcriptional levels depending on the extent of com-plementation between miRNA and mRNA. To date, a large number of miRNAs have been reported in many species, but none for eggplant (Solanum melongena L.). In this paper, a computational homology search approach based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. The search was started with the known plant miRNAs compared to eggplant expressed sequence tags (EST) databases to find potential miRNAs. Following a range of filtering criteria, a total of 16 potential miRNAs belonging to 12 families were identified. Three pairs of sense and antisense strand eggplant miRNAs belonging to three different miRNA families were also found. Furthermore, miR390 and miR399 sense/antisense pairs are identified for the first time in plants. Using online software psRNATarget, we further predicted the target genes of these 16 miRNAs and got 71 potential targets genes on base of 15 eggplant miRNAs. Most of these target genes were predicted to encode proteins that play key role in eggplant growth, de-velopment, metabolism, and stress responses.

Key words: target gene, bioinformatics, EST, eggplant(Solanum melongena L.), microRNAs (miRNAs)

张磊，晁江涛，崔萌萌，陈雅琼，宗鹏，孙玉合. 茄子microRNAs与其靶基因的生物信息学预测[J]. 遗传, 2011, 33(7): 776-784.

ZHANG Lei, CHAO Jiang-Chao, CUI Meng-Meng, CHEN Ya-Qiong, ZONG Feng, SUN Yu-Ge. Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)[J]. HEREDITAS, 2011, 33(7): 776-784.

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茄子microRNAs与其靶基因的生物信息学预测

Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)

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