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Updated: Aug 2, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs
Jingjing Jin1, Peng Lu1, Yalong Xu1
1China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
Nucleic Acids Research
|October 20, 2020
Summary
The Plant Long noncoding RNA Database (PLncDB) V2.0 now offers comprehensive data for 80 plant species, enhancing lncRNA research with uniform annotations and visualization tools.
Area of Science:
- Plant molecular biology
- Bioinformatics
- Genomics
Background:
- Long noncoding RNAs (lncRNAs) play crucial roles in plant gene regulation.
- Existing plant lncRNA databases have limitations in data coverage, annotation consistency, and functional information.
- A unified and comprehensive resource is needed for plant lncRNA research.
Purpose of the Study:
- To upgrade and expand the Plant Long noncoding RNA Database (PLncDB) to address current deficiencies.
- To provide a comprehensive, user-friendly resource for plant lncRNA data mining and functional exploration.
- To integrate diverse lncRNA information, including expression patterns and epigenetic data.
Main Methods:
- Developed a uniform annotation pipeline for lncRNA identification and characterization.
- Integrated data from RNA-Seq datasets and existing lncRNA resources (e.g., EVLncRNAs, RNAcentral).
- Implemented visualization tools (JBrowse, eFP Browser, EPexplorer) for expression and epigenetic data.
Main Results:
- PLncDB V2.0 contains over 1.2 million lncRNAs from 80 plant species.
- The database integrates data from 13,834 RNA-Seq datasets.
- Includes visualization tools for expression patterns and epigenetic signals, alongside target and regulatory network information.
Conclusions:
- PLncDB V2.0 provides a significantly enhanced and comprehensive resource for plant lncRNA research.
- The database facilitates data mining and functional studies in plant genomics.
- It serves as a valuable tool for the plant lncRNA community.
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