Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).
Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).
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DOI：
10.1261/rna.045799.114
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发表时间：
2015-02
期刊：
影响因子：
--
通讯作者：
Kanai A
中科院分区：
文献类型：
--
作者：
Ikeda KT;Hirose Y;Hiraoka K;Noro E;Fujishima K;Tomita M;Kanai A
MicroRNA已在各种模式物种中被鉴定和分析，但为了更全面地了解miRNA的进化，需要对非模式物种中的miRNA进行研究。在这项研究中，我们研究了非模式物种Triops cancriformis（蝌蚪虾）的miRNA，这是一种“活化石”，其形态在近2亿年内没有改变。戏剧性的个体发生变化发生在其发展过程中。为了阐明miRNAs的进化，我们比较分析了miRNAs及其RNAi机制的组成部分。我们使用深度测序来分析来自T. cancriformis（卵、第一至第四龄和成虫），并利用深度测序分析了其基因组DNA。我们鉴定了180个miRNAs（87个保守的miRNAs和93个新的候选miRNAs），并推导出其RNAi机制的组成部分：DICER 1，AGO 1 -3，PIWI和AUB蛋白。比较T. cancriformis和Drosophila melanogaster的四个保守的miRNAs的表达模式不一致。这表明，尽管两个物种的miRNA序列非常相似，但它们的作用在物种之间存在差异。miRNA保守性分析显示，大部分保守的T. cancriformis miRNAs与节肢动物的miRNAs具有序列相似性，尽管T.癌症被称为“活化石”。然而，我们发现T. cancriformis与脊椎动物比节肢动物更相似。这些结果提示T.癌形菌以独特的方式进化。
MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a “living fossil,” whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed its miRNAs and the components of its RNAi machinery. We used deep sequencing to analyze small RNA libraries from the six different developmental stages of T. cancriformis (egg, first–fourth instars, and adult), and also analyzed its genomic DNA with deep sequencing. We identified 180 miRNAs (87 conserved miRNAs and 93 novel candidate miRNAs), and deduced the components of its RNAi machinery: the DICER1, AGO1–3, PIWI, and AUB proteins. A comparative miRNA analysis of T. cancriformis and Drosophila melanogaster showed inconsistencies in the expression patterns of four conserved miRNAs. This suggests that although the miRNA sequences of the two species are very similar, their roles differ across the species. An miRNA conservation analysis revealed that most of the conserved T. cancriformis miRNAs share sequence similarities with those of arthropods, although T. cancriformis is called a “living fossil.” However, we found that let-7 and DICER1 of T. cancriformis are more similar to those of the vertebrates than to those of the arthropods. These results suggest that miRNA systems of T. cancriformis have evolved in a unique fashion.
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