PNRD: a plant non-coding RNA database

Abstract

The first ncRNA found was an alanine tRNA in baker's yeast, and the first detected microRNAs (miRNAs) promoted ncRNA research to a whole new level. Research on ncRNAs in animals has focused on the medical field, while in plant scientists are more concerned with improving agronomic traits. In 2010, we constructed a plant miRNA database named PMRD to meet the demand for miRNA research in plants. To provide a way to do fundamental research on plant ncRNAs and take full advantage of tremendous public resources, we designed an updated platform called plant ncRNA database (PNRD) based on its predecessor PMRD, which is accessible at http://structuralbiology.cau.edu.cn/PNRD. We collected a total of 25739 entries of 11 different types of ncRNAs from 150 plant species. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.

Figure 1.

The expression profile of the MIR156 family in five species: grape, sorghum, maize, tomato and Populus, respectively. The x-axis represents different tissues in one species while the y-axis represents the normalized reads count of miR156 in corresponding tissue. The read counts were calculated by the localized miRanalyzer toolkit.

Figure 2.

Structure of PNRD database, composed of five parts: Search section, Browse section, Tools section, Download page and Help page.

Figure 3.

Analysis pipeline and corresponding results of ath-miR172 using PNRD database. We use a pipeline to demonstrate how to do research with PNRD using different functional tools. (A) Results of keyword search on search page using ‘flowering time control’ as input. PNRD gives users the most matched ncRNAs with supportive literature containing their input. (B) The alignment results of ath-miR172c and its targets using psRNAtarget software and text-mining, which includes not only coding mRNAs, but also target mimics. (C) Information on literature from the text-mining pool with an intimate association with ath-miR172c and some important relevant knowledge. (D) Expression profiles of ath-miR172c. The left frame is the profile projects containing ath-miR172c using ‘search in exprofile’ section of the Search page. The other two histograms summarize results of the expression profile as searched above. The upper histogram reflects the MIR172 family expression profile derived from a project named ‘MicroRNA activity in the Arabidopsis male germline’. The x-axis represents five members of the MIR172 family while the y-axis is normalized read counts expressed in three different tissues, identified in three different colors. The lower histogram was derived from six different projects. The x-axis represents different experimental conditions and the y-axis represents normalized read counts. Different colors are used to identify different projects. (E) Basic information about ath-miR172c, such as the genomic location, sequence and secondary structure. (F) Customized UCSC Genome Browser screenshot of ath-miR172c. Five histone marks from two data sets of GEO (GSE50636: H3K27me3, H3K4me3; and GSE657: H3K4me1, H3K4me2 and H3K4me3) are near ath-miR172c. Data were downloaded from GEO database and calculated in-house to display in UCSC.