State Key Laboratory of Plant Physiology and Biochemistry and State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
Nucleic Acids Res. 2010 Jan;38(Database issue):D806-13. doi: 10.1093/nar/gkp818. Epub 2009 Oct 6.
MicroRNAs (miRNA) are approximately 21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.
微小 RNA（miRNA）是大约 21 个核苷酸长的非编码小分子 RNA，作为真核生物转录后的调控因子发挥作用。miRNA 在调节植物生长和发育中起着至关重要的作用。近年来，miRNA 作用机制和后果的研究取得了巨大进展。随着拟南芥、水稻、杨树、大豆等植物全基因组序列的出现，通过整合大量公共 miRNA 数据信息，开发一个植物 miRNA 数据库是可取的。植物 miRNA 数据库（PMRD）整合了公共数据库中已有的 miRNA 数据，从最近的文献中提取，并生成了内部数据。该数据库包含序列信息、二级结构、靶基因、表达谱和基因组浏览器。在 PMRD 中，共收集了来自 121 种植物的 8433 个 miRNA，包括模式植物和主要作物，如拟南芥、水稻、小麦、大豆、玉米、高粱、大麦等。对于拟南芥、水稻、杨树、大豆、棉花、紫花苜蓿和玉米，我们在数据库中包含了每个 miRNA 的可能靶基因，以及在数据库中预测的相互作用位点。此外，我们在 PMRD 中提供了 miRNA 表达谱，包括我们的本地水稻氧化应激相关微阵列数据（LC Sciences miRPlants_10.1）和最近公布的杨树、拟南芥、番茄、玉米和水稻的微阵列数据。PMRD 数据库是利用开源技术构建的，采用用户友好的网络界面和多种搜索工具。PMRD 可在 http://bioinformatics.cau.edu.cn/PMRD 免费获取。我们希望 PMRD 成为 miRNA 领域科学家的一个有用工具，以研究 miRNA 及其靶基因的功能，特别是在模式植物和主要作物中。
