Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust.
Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust.
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蝗虫两个阶段小 RNA 转录组的表征和比较分析
DOI：
10.1186/gb-2009-10-1-r6
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Kang L
中科院分区：
文献类型：
--
作者：
Wei Y;Chen S;Yang P;Ma Z;Kang L
背景昆虫小RNA的研究报道主要来自全变态昆虫，且已有全变态昆虫的基因组序列数据。因此，对昆虫半代谢小RNA的研究可以为昆虫小RNA的进化和功能提供更多的信息。蝗虫是一种重要的半变态害虫，对经济有很大的危害。它的相位变化，作为一种表型可塑性，从差异基因表达可能在转录后水平，介导的小RNA，和transformational level.ResultsHere，使用高通量测序，我们的特点是小RNA转录组中的蝗虫。我们通过miRBase相似性搜索确定了50个保守的microRNA家族，并且使用我们新开发的独立于蝗虫基因组序列的方法确定了最多185个潜在的蝗虫特异性microRNA家族候选者。我们还证明了microRNA的保守性 *，蝗虫microRNA的进化分析表明，蝗虫中miRNA的产生沿着三个系统发育树分支集中：两侧对称动物、体腔动物和昆虫。我们的研究鉴定了数千种内源性小干扰RNA，其中一些是转座子来源的，还检测到许多Piwi相互作用的RNA样小RNA。两个时期小RNA表达模式的比较表明，在孤立期，较长的小RNA表达量更高，而每类小RNA在两个时期之间表现出不同的表达谱。小分子RNA在这两个阶段的差异表达可能进一步揭示了阶段变化的分子机制。
BackgroundAll the reports on insect small RNAs come from holometabolous insects whose genome sequence data are available. Therefore, study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in insects. The locust is an important, economically harmful hemimetabolous insect. Its phase changes, as a phenotypic plasticity, result from differential gene expression potentially regulated at both the post-transcriptional level, mediated by small RNAs, and the transcriptional level.ResultsHere, using high-throughput sequencing, we characterize the small RNA transcriptome in the locust. We identified 50 conserved microRNA families by similarity searching against miRBase, and a maximum of 185 potential locust-specific microRNA family candidates were identified using our newly developed method independent of locust genome sequence. We also demonstrate conservation of microRNA*, and evolutionary analysis of locust microRNAs indicates that the generation of miRNAs in locusts is concentrated along three phylogenetic tree branches: bilaterians, coelomates, and insects. Our study identified thousands of endogenous small interfering RNAs, some of which were of transposon origin, and also detected many Piwi-interacting RNA-like small RNAs. Comparison of small RNA expression patterns of the two phases showed that longer small RNAs were expressed more abundantly in the solitary phase and that each category of small RNAs exhibited different expression profiles between the two phases.ConclusionsThe abundance of small RNAs in the locust might indicate a long evolutionary history of post-transcriptional gene expression regulation, and differential expression of small RNAs between the two phases might further disclose the molecular mechanism of phase changes.
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LocustDB：迁徙蝗虫（colcusta偏偏）转录组和生物学的关系数据库。
影响因子：
4.4
作者：
Ma, Zongyuan;Yu, Jun;Kang, Le
通讯作者：
Kang, Le
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
影响因子：
64.5
作者：
Lewis, BP;Shih, IH;Burge, CB
通讯作者：
Burge, CB
影响因子：
64.5
作者：
Boquet, I;Boujemaa, R;Préat, T
通讯作者：
Préat, T
DOI：
10.1073/pnas.0407753101
发表时间：
2004-12-21
影响因子：
11.1
作者：
Kang, L;Chen, XY;Yu, J
通讯作者：
Yu, J