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.

Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing

“…Although tRNAs and snoRNAs were considered as two of the largest classes of non-protein-coding RNAs (Schattner et al 2005), no significant sequence similarity was found between banana lncRNAs and tRNAs and snoRNAs of other species. To make stringent classification, lncRNAs were once again mapped to all species of plant small RNA families available at the PNRD database (Yi et al 2015) separately, such as miRNA stem loop precursors, mature miRNA, snoRNAs, and trans-acting siRNA (tasiRNA). One lncRNA, MUSA-T-NC506, was found to have significant homology to microRNA-156 considered as microRNA-156 precursors.…”

“…Xin et al (2011) identified 125 putative stress-responsive lncRNAs in response to powdery mildew infection and heat stress in wheat leaves. Twenty-two putative salt-and water-deficit stress-responsive lncRNA were identified in Arabidopsis (Xin et al 2011 (Yi et al 2015).…”

Analysis of Rice Genome Long Non-Coding RNA Sequences

“…Biotechnological improvement of crops necessitates a deeper understanding of the structure and functions of lncRNAs [17]. In the present study, lncRNAs from rice genome have been collected from three important databases namely, GreeNC [18], PNRD [19] and plnLNCRBase [20], and functionally annotated based on bioinformatics approach.…”

PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs)

“…Although, a number of lncRNA databases such as TAIR (for Arabidopsis) [21], PlantNATsDB (natural antisense transcripts) [22], lncRNAdb (functional lncRNA database) [10], NONCODE (noncoding RNAs in only Arabidopsis as plant species) [23], PLncDB (with a limited number of lncRNAs in only Arabidopsis) [24], GreeNC (lncRNA repository in plants and algae) [25], CANTATAdb (lncRNA database covering ten plant species) [26] and PNRD for non-coding RNAs in four plant species [27] are available, except miRSponge covering only a very limited number of eTM data for Arabidopsis thaliana [28], there is no any comprehensive available database specifically developed for plant eTMs yet. To provide a high quality tool for plant scientist that can accelerate the research on this unique class of transcripts, we established an online database called PeTMbase, which deposits computationally predicted eTMs in plants.…”