Yang Kun, Wen Xiaopeng, Mudunuri Suresh B, Sablok Gaurav
Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, China.
Centre for Bioinformatics Research, SRKR Engineering College, Bhimavaram, India.
Front Plant Sci. 2019 Jan 22;9:1881. doi: 10.3389/fpls.2018.01881. eCollection 2018.
microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs:target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. Plant isomiR Atlas is available at www.mcr.org.in/isomir. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.
微小RNA（miRNA）作为关键调控因子发挥着重要作用，控制着植物在整个发育过程、非生物和生物胁迫、组织极性中的转录后事件，也在定义转录后机制起源的进化基础方面发挥作用。随着下一代测序方法的出现，识别受调控和共同调控的小RNA模式，特别是miRNA及其序列变体，已广泛证明了miRNA及其时间调控在维持植物发育及其对胁迫条件反应中的作用。尽管经典miRNA的作用已得到广泛探索并揭示了功能多样性，但关于异源miRNA（isomiR）的研究仍然有限，迫切需要在整个植物界开展相关工作。关于异源miRNA的这种相对信息缺乏可能归因于缺乏跨广泛植物物种的大规模异源miRNA检测方法。在本研究中，我们通过开发植物异源miRNA图谱（Plant isomiR Atlas）来解决这一问题，该图谱利用677个小RNA数据集对23种植物物种进行了大规模异源miRNA检测，共从6167个前体中鉴定出98374个模板化和非模板化的异源miRNA。植物异源miRNA图谱提供了多种可视化功能，如物种特异性异源miRNA、异源miRNA与经典miRNA的重叠、末端修饰分类、使用psRNATarget和TargetFinder进行靶标识别以及经典miRNA与靶标的相互作用。植物异源miRNA图谱将在理解miRNA组的调控性质方面发挥关键作用，并将加速对异源miRNA功能作用的理解。植物异源miRNA图谱可在www.mcr.org.in/isomir获取。植物异源miRNA图谱将在理解miRNA组的调控性质方面发挥关键作用，并将加速对植物异源miRNA功能靶标的理解和多样性研究。
