China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco, Guiyang 550081, China.
Nucleic Acids Res. 2021 Jan 8;49(D1):D1489-D1495. doi: 10.1093/nar/gkaa910.
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb.tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five built-in search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.
长链非编码 RNA（lncRNA）是指长度大于 200 个核苷酸且几乎没有蛋白编码潜能的转录本。lncRNA 数量不断增加，其在植物中的功能也得到了越来越多的证实，这使得人们需要创建一个综合性的 lncRNA 研究数据库。然而，现有的植物 lncRNA 数据库存在一些缺陷，包括一些模式植物的 lncRNA 数据缺失、注释标准不均匀、表达模式缺乏可视化以及缺乏表观遗传信息。为了克服这些问题，我们对基于统一注释流程的 Plant Long noncoding RNA Database（PLncDB，http://plncdb.tobaccodb.org/）进行了升级。PLncDB V2.0 目前包含 80 个植物物种的 1 246 372 条 lncRNA，基于 13 834 个 RNA-Seq 数据集，整合了包括 EVLncRNAs、RNAcentral 等其他四个资源的 lncRNA 信息。使用多种工具（JBrowse、eFP Browser 和 EPexplorer）可以可视化表达模式和表观遗传信号。还提供了 lncRNA 的靶标和调控网络，用于功能探索。此外，PLncDB V2.0 具有层次结构和用户友好性，内置了 5 个搜索引擎。我们相信 PLncDB V2.0 对植物 lncRNA 研究社区和数据挖掘研究非常有用，为植物中基于数据驱动的 lncRNA 研究提供了一个综合性资源。
