MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish
MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish
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DOI：
10.1093/molbev/msz168
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发表时间：
2019-11-01
影响因子：
10.7
通讯作者：
Meyer, Axel
中科院分区：
文献类型：
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作者：
Franchini, Paolo;Xiong, Peiwen;Meyer, Axel
慈鲷鱼提供教科书的爆炸性表型多样化和同域物种形成的例子，从而使它们成为研究快速谱系分化的分子机制的理想系统。尽管事实上，基因调控提供了基因功能和物种形成的多样化之间的关键联系，许多基因组调控机制，如microRNA（miRNA）在这些迅速多样化的群体很少受到关注。因此，我们研究了miRNAs在米达斯慈鲷（Amphilophus spp.）从巴拿马火山口湖。利用来自五个迈达斯物种的胚胎的miRNA和mRNA测序，我们首先确定了mRNA中的miRNA结合位点，并强调了这些适应性辐射物种中惊人数量的新型miRNA的存在。然后，通过对表达水平的分析，我们确定了假定的miRNA/基因靶对，其表达水平与miRNA在下调mRNA中的作用一致。此外，我们确定，几个miRNA/基因对显示收敛的表达模式与重复的底栖/湖沼同域物种的分歧暗示这些miRNA作为潜在的分子机制复制同域分歧。最后，由于这些候选miRNA/基因对可能在这些慈鲷的表型多样化中发挥核心作用，我们通过原位杂交表征了所选miRNA及其靶基因的表达结构域，进一步证明miRNA调控可能在Midas慈鲷适应性辐射中发挥作用。这些结果为以下假设提供了支持：即使在存在基因流的情况下，极其快速进化的miRNA调控也会导致快速进化分歧。
Cichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.