PLncDB

Overview

PLncDB (Plant Long noncoding RNA Database) is a comprehensive encyclopedia of plant long noncoding RNAs, providing a centralized resource for plant lncRNA research. The database uses uniform annotation standards to systematically catalog lncRNAs across phylogenetically diverse plant species.

Database Content

Current version (V2.0, released 2020) contains:

• 1,246,372 lncRNAs annotated across 80 plant species
• Species ranging from chlorophytes to angiosperms (16 monocotyledons, 53 eudicotyledons)
• 13,834 RNA-Seq datasets from diverse tissues, developmental stages, and stress treatments
• 456 epigenetic modification datasets (H3K27me3, H3K4me3, H3K36me3, H3K9me3)
• Integration of validated lncRNAs from EVLncRNAs
• Plant lncRNA candidates from RNAcentral

Annotation Pipeline

PLncDB uses a standardized pipeline for lncRNA identification:

• Transcriptome assembly using StringTie from HISAT2-aligned reads
• Filtering criteria: >200nt length, <120aa ORF
• Coding potential assessment using CPC, PLEK, RNAplonc, and CREMA (candidates must satisfy ≥2 criteria)
• High-confidence lncRNAs satisfy ≥3 criteria
• Removal of transcripts overlapping with rRNA, tRNA, sRNA, and miRNA

Key Features

Expression Analysis

• TPM-normalized expression values across all datasets
• Tissue-specific expression identification (ROKU method, cutoff 0.8)
• Expression patterns across different tissues, developmental stages, mutants, and stress treatments

Target Prediction

• miRNA-mRNA interactions predicted by psRobot
• lncRNA-miRNA mimicry predicted by psMimic
• lncRNA-protein interactions predicted by IntaRNA

Epigenetic Information

• Histone modification profiles (H3K27me3, H3K4me3, H3K36me3, H3K9me3)
• Expression changes in RdRM-related mutants (RDD, DCL1/2/3/4, AGO4, RDR2, DMS1)

Visualization Tools

JBrowse

Genome browser for exploring:

• lncRNA genomic locations
• Expression patterns
• Epigenetic modification signals
• Flanking genomic regions

eFP Browser

Electronic Fluorescent Pictograph browser for visualizing tissue-specific expression patterns of individual lncRNAs.

EPexplorer

Expression landscape visualization tool for:

• Batch lncRNA expression analysis
• Identification of tissue-specific candidates
• Heatmap visualization across samples

Search Capabilities

PLncDB provides five search engines:

1. Keyword search - search all database fields
2. Sequence BLAST - similarity search against lncRNA sequences
3. Genome coordinates - search by genomic location
4. Expression values - search by expression level
5. Tissue-specific search - find tissue-specific lncRNAs

Data Access

Browse

• Hierarchical browsing by species
• Summary information (genome version, lncRNA counts, dataset numbers)
• Detailed lncRNA pages with 6 sections: basic info, sequence, secondary structure, genomic map, regulatory network, expression patterns

Download

• FTP bulk download of all data
• User-defined download by species and data type
• Quick access for genome coordinates
• Backup copy available on Zenodo (ID: 4017591)
• Download formats: FASTA, CSV, GFF

Submit

Community submission portal for plant lncRNAs with required information for inclusion in standard annotation pipeline.

Model Plants Covered

Includes major model species:

• Arabidopsis thaliana
• Oryza sativa (rice)
• Zea mays (maize)
• Glycine max (soybean)
• Solanum lycopersicum (tomato)
• Solanum tuberosum (potato)
• Nicotiana tabacum (tobacco)

Technical Implementation

Database built using:

• Python programming language
• Vue.js frontend framework
• ElementUI interface components
• Django web framework
• Nginx proxy services
• Echarts for graph visualization
• Cytoscape for network visualization

Updates

PLncDB is updated semi-annually with:

• Integration of data from other databases
• Community submissions
• New plant species annotations
• Updated RNA-Seq datasets

Citation

If using PLncDB in your research, please cite:

Jin J, Lu P, Xu Y, Li Z, Yu S, Liu J, Wang H, Chua NH, Cao P. PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs. Nucleic Acids Research, 2021, 49(D1):D1489-D1495. doi:10.1093/nar/gkaa910