Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors
Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors
复制标题
DOI：
10.1007/s10142-016-0487-y
复制
发表时间：
2017-05-01
影响因子：
2.9
通讯作者：
Budak, Hikmet
中科院分区：
文献类型：
--
作者：
Alptekin, Burcu;Budak, Hikmet
MicroRNA 是转录后基因调控的关键参与者，对细胞生命的基本过程具有深远的影响。它们的识别和表征以及它们的靶标对于探索和利用它们在功能环境中的作用具有重要意义，为重要生物过程（例如应激耐受性或环境适应）的调节提供了有价值的线索。小麦是一种耐寒作物，在温带地区广泛收获，是人类饮食的主要组成部分。随着下一代测序技术的出现，每个碱基对的测序成本大大降低，来自多个小麦品种（包括祖先和野生近缘种）的基因组和转录组数据已经变得可用。在本研究中，我们通过利用公开的转录组数据，对面包小麦 (Triticum aestivum L.) 及其二倍体祖先和近缘品种 Aegilops sharonensis、Aegilops speltoides、Aegilops tauschii、Triticum monococum 和 Triticum urartu 的 microRNA 库进行了计算机识别和比较分析。超过 200 个 miRNA 家族被鉴定出来，其中大部分以前从未被报道过。祖先关系拓展了我们对小麦 miRNA 进化的理解，而单球菌 miRNA 为了解驯化对 miRNA 表达的影响提供了重要线索。野生伊蚊的比较分析。 sharonensis 种质强调了与胁迫耐受性相关的候选 miRNA。面包小麦及其二倍体祖先和近缘种的 miRNA 库为了解 miRNA 基因的多样性和分布提供了重要的见解，这将有助于阐明禾本科家族的 miRNA 进化。彻底了解不同遗传背景下 miRNA 的趋同和趋异表达谱可以为调节基因调控以获得更好的作物性能提供独特的机会。
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.