Integrated Analysis of miRNAome and Transcriptome Identify Regulators of Elm Seed Aging.
Integrated Analysis of miRNAome and Transcriptome Identify Regulators of Elm Seed Aging.
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DOI：
10.3390/plants12081719
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发表时间：
2023-04-20
期刊：
影响因子：
--
通讯作者：
Xue H
中科院分区：
文献类型：
--
作者：
Ye T;Huang X;Ma T;Li Y;Wang X;Lu H;Xue H
成熟后，种子活力不可逆转地下降。了解潜在机制对于种质保存很重要。 MicroRNA (miRNA) 在植物中发挥着重要的调节作用。然而，人们对 miRNA 如何调节种子老化知之甚少。在这里，对三个老化阶段的榆树（Ulmus pumila L.）种子进行了包括转录组、小RNA组和降解组在内的多组学分析，以寻找种子老化的调节因子。在小RNAome中，鉴定出119个miRNA，其中包括111个保守miRNA和8个针对榆树种子的新型miRNA，命名为upu-miRn1-8。在种子老化过程中共鉴定出 4900 个差异表达基因、22 个差异表达 miRNA 和 528 个 miRNA 靶点对。靶基因主要涉及内质网蛋白质加工、代谢、植物激素信号转导和剪接体等。通过 qRT-PCR 验证了几种 DEG 和 miRNA 的表达。降解组数据显示了upu-miR399a对ABCG25和upu-miR414a对GIF1等的准确降解位点。双荧光素酶实验验证了烟叶中upu-miR399a对ABCG25和upu-miR414a对GIF1的负调控。本研究概述了种子老化过程中mRNA、miRNA和miRNA靶基因的调控网络，有助于在转录和转录后水平整合种子活力的调控机制。
After maturity, seed vigor irreversibly decreases. Understanding the underlying mechanism is important to germplasm preservation. MicroRNAs (miRNAs) play vital regulatory roles in plants. However, little is known about how miRNAs regulate seed aging. Here, elm (Ulmus pumila L.) seeds of three aging stages were subjected to a multi-omics analysis including transcriptome, small RNAome and degradome, to find regulators of seed aging. In the small RNAome, 119 miRNAs were identified, including 111 conservative miRNAs and eight novel miRNAs specific to elm seeds, named upu-miRn1-8. A total of 4900 differentially expressed genes, 22 differentially expressed miRNAs, and 528 miRNA-target pairs were identified during seed ageing. The target genes were mainly involved in the processing of proteins in the endoplasmic reticulum, metabolism, plant hormone signal transduction, and spliceosome. The expression of several DEGs and miRNAs were verified by qRT-PCR. The degradome data showed the exact degradation sites of upu-miR399a on ABCG25, and upu-miR414a on GIF1, etc. The dual-luciferase assay verified the negative regulation of upu-miR399a on ABCG25 and upu-miR414a on GIF1 in tobacco leaves. This study outlined the regulation network of mRNA, miRNA and miRNA-target genes during seed aging, which is helpful in integrating the regulation mechanisms of seed vigor at the transcriptional and post-transcriptional levels.
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