Beijing Academy of Agriculture and Forestry Sciences, China.
Peking University and Beijing Academy of Agriculture and Forestry Sciences, China.
Brief Bioinform. 2021 Sep 2;22(5). doi: 10.1093/bib/bbab075.
Last two decades, the studies on microRNAs (miRNAs) and the numbers of annotated miRNAs in plants and animals have surged. Herein, we reviewed the current progress and challenges of miRNA annotation in plants. Via the comparison of plant and animal miRNAs, we pinpointed out the difficulties on plant miRNA annotation and proposed potential solutions. In terms of recalling the history of methods and criteria in plant miRNA annotation, we detailed how the major progresses made and evolved. By collecting and categorizing bioinformatics tools for plant miRNA annotation, we surveyed their advantages and disadvantages, especially for ones with the principle of mimicking the miRNA biogenesis pathway by parsing deeply sequenced small RNA (sRNA) libraries. In addition, we summarized all available databases hosting plant miRNAs, and posted the potential optimization solutions such as how to increase the signal-to-noise ratio (SNR) in these databases. Finally, we discussed the challenges and perspectives of plant miRNA annotations, and indicated the possibilities offered by an all-in-one tool and platform according to the integration of artificial intelligence.
在过去的二十年中，人们对 microRNAs（miRNAs）的研究以及动植物中注释的 miRNAs 数量呈爆炸式增长。在此，我们综述了植物中 miRNA 注释的最新进展和挑战。通过比较植物和动物 miRNA，我们指出了植物 miRNA 注释的困难，并提出了潜在的解决方案。在回顾植物 miRNA 注释方法和标准的历史时，我们详细介绍了主要进展是如何取得并不断发展的。通过收集和分类植物 miRNA 注释的生物信息学工具，我们调查了它们的优缺点，特别是那些通过解析深度测序的小 RNA（sRNA）文库来模拟 miRNA 生物发生途径的工具。此外，我们总结了所有可用的植物 miRNA 数据库，并提出了潜在的优化解决方案，例如如何提高这些数据库中的信噪比（SNR）。最后，我们讨论了植物 miRNA 注释的挑战和前景，并根据人工智能的整合指出了一体化工具和平台所提供的可能性。
