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AlnC: An extensive database of long non-coding RNAs in angiosperms
Ajeet Singh1, A T Vivek1, Shailesh Kumar1
1Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
Plos One
|April 14, 2021
Summary
A new web tool, AlnC, catalogs over 10 million long non-coding RNA (lncRNA) transcripts from 682 plant species. This resource aids research into plant development and gene regulation.
Area of Science:
- Plant molecular biology
- Genomics
- Bioinformatics
Background:
- Long non-coding RNAs (lncRNAs) are critical regulators of plant cellular processes.
- Despite available sequencing data, lncRNAs in many Angiosperm species remain underexplored.
- A comprehensive catalog is needed to facilitate lncRNA research in plants.
Purpose of the Study:
- To develop a user-friendly, open-access web interface for exploring Angiosperm lncRNAs.
- To provide a centralized resource for lncRNA data from diverse plant species.
- To facilitate research on lncRNA functions and potential applications in agriculture.
Main Methods:
- Utilized the 1000 Plant (1KP) transcriptomes data.
- Developed the AlnC (Angiosperm lncRNA Catalogue) web interface.
- Annotated lncRNA transcripts and identified potential small open reading frames (sORFs).
Main Results:
- AlnC currently houses 10,855,598 annotated lncRNA transcripts.
- The database covers 682 Angiosperm plant species and 809 tissues.
- Features include browsing, searching, downloading, interactive graphs, and an online BLAST service.
Conclusions:
- AlnC provides a rich, accessible resource for lncRNA research in flowering plants.
- The tool is expected to advance studies on lncRNA roles in plant development and gene regulation.
- AlnC can aid in improving economically important plant traits.
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