Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan 701, Taiwan.
Plant Cell Physiol. 2020 Jun 1;61(6):1204-1212. doi: 10.1093/pcp/pcaa034.
Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/.
小 RNA（sRNA），如 microRNA（miRNA）和短干扰 RNA，已被广泛认知可通过降解靶 mRNA 来控制植物中的基因表达。大量研究已应用下一代测序（NGS）来揭示植物 sRNA 的调控途径。因此，已经开发了许多生物信息学工具来分析 sRNA NGS 数据。然而，大多数方法都集中在 sRNA 表达谱的研究或新的 miRNA 预测上。sRNA 靶基因的分析通常未集成到它们的流程中。因此，目前还没有办法识别宿主与病毒之间的相互作用机制或两种病毒之间的协同效应。在本研究中，开发了一个名为 Small RNA Illustration System（sRIS）的综合系统。该系统包含两个主要组件。第一个组件用于 sRNA 概述分析，不仅可以识别 miRNA，还可以研究病毒衍生的小干扰 RNA。第二个组件用于 sRNA 靶标预测，它结合了生物信息学计算和降解组测序数据，以提高靶标预测的准确性。此外，该系统的设计使得每个分析的输出的图形和表格都可以轻松检索和访问，使用户更容易快速识别和量化他们的结果。sRIS 可在 http://sris.itps.ncku.edu.tw/ 获取。
