Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication
Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication
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大豆驯化过程中 MIRNA 基因和 microRNA 靶标协同进化的全球调查
DOI：
10.1111/tpj.13113
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发表时间：
2016-02-01
期刊：
影响因子：
7.2
通讯作者：
Tian, Zhixi
中科院分区：
文献类型：
--
作者：
Liu, Tengfei;Fang, Chao;Tian, Zhixi
虽然植物驯化过程中编码基因的选择已经得到了很好的研究，但MIRNA基因（MIRs）的进化以及microRNA（miRNAs）与其靶标之间的相互作用在这一过程中知之甚少。在这里，我们提出了一个全基因组范围内的调查选择的MIRs和miRNA的目标在大豆驯化和改进。我们的研究结果表明，总体而言，MIRs比miRNA靶标具有更高的进化速率。尽管如此，它们在大豆驯化过程中确实表现出某些相似的进化模式：具有高表达和复制状态的MIRs和miRNA靶标，以及具有更多配偶体的MIRs和miRNA靶标，与没有这些特征的对应物相比，表现出较低的核苷酸分歧，这表明表达水平，复制状态和miRNA-靶标相互作用对于MIRs和miRNA靶标的进化至关重要。进一步的研究表明，受到强纯化选择的miRNA-靶对比那些表现出遗传多样性的miRNA-靶对具有更大的相似性。此外，通过驯化和改良，栽培大豆群体中大量miRNA-靶标对的相似性比野生大豆群体中的那些增加，而少数miRNA-靶标对表现出降低的相似性，这可能与特定驯化性状的采用有关。总之，我们的研究结果揭示了大豆驯化过程中MIRs和miRNA靶标的共同进化。
Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA-target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA-target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA-target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA-target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co-evolution of MIRs and miRNA targets during soybean domestication.