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Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Andrew D L Nelson1, Upendra K Devisetty2, Kyle Palos1
1Beilstein Lab, School of Plant Sciences, University of ArizonaTucson, AZ, USA.
Frontiers in Genetics
|May 25, 2017
Summary
Evolinc is a new pipeline for discovering long intergenic non-coding RNAs (lincRNAs) and analyzing their evolution. It aids in identifying novel lincRNAs and understanding their conservation across species, revealing evolutionary events like duplication and loss.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Long intergenic non-coding RNAs (lincRNAs) are abundant and diverse, but their evolutionary origins and persistence remain understudied.
- Existing lincRNA studies are often limited to specific species, hindering comparative evolutionary analyses.
Purpose of the Study:
- To present Evolinc, a novel two-module pipeline for lincRNA discovery and evolutionary characterization.
- To facilitate the identification and evolutionary analysis of lincRNAs across diverse species.
Main Methods:
- Evolinc-I: A workflow for lincRNA identification, differential expression analysis, and genome browser visualization.
- Evolinc-II: A comparative genomics and transcriptomics workflow to assess lincRNA locus conservation across related species.
- Validation using Arabidopsis and human lincRNA datasets, and evolutionary analysis of Brassicaceae lincRNAs and human TERC.
Main Results:
- Evolinc-I successfully identified novel lincRNAs in Arabidopsis (70) and human (43) datasets.
- Evolinc-II narrowed down 5,361 Arabidopsis lincRNAs to 40 conserved within Brassicaceae species.
- Analysis of human TERC revealed complex evolutionary events, including duplication and locus loss/acquisition in rodent lineages.
Conclusions:
- The Evolinc pipeline is a valuable tool for lincRNA discovery and evolutionary studies.
- Evolinc facilitates the identification of conserved lincRNAs and the reconstruction of their evolutionary histories.
- The pipeline revealed novel insights into lincRNA evolution, including dynamic locus changes.
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