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Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq.

A T Vivek1, Shailesh Kumar2

  • 1National Institute of Plant Genome Research in New Delhi, India.

Briefings in Bioinformatics
|December 17, 2020
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Summary

This review details plant non-coding RNAs (ncRNAs) and computational methods for their discovery using RNA sequencing (RNA-seq). It provides a bioinformatics toolbox to aid researchers in identifying and annotating these crucial regulatory molecules.

Keywords:
RNA-seqcircRNAlncRNAmiRNAncRNAssRNA-seqsiRNAtsRNA

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Area of Science:

  • Plant molecular biology
  • Bioinformatics
  • Genomics

Background:

  • Plant transcriptomes contain diverse regulatory non-coding RNAs (ncRNAs) vital for physiological processes.
  • The functions of most plant ncRNAs remain largely uncharacterized despite their ubiquity.
  • Genome-wide identification and annotation of ncRNAs are essential for understanding plant biology.

Purpose of the Study:

  • To review major classes of plant endogenous regulatory ncRNAs.
  • To discuss computational strategies for discovering ncRNAs from RNA sequencing data.
  • To provide a bioinformatics toolbox for plant ncRNA research.

Main Methods:

  • Analysis of high-throughput RNA sequencing (RNA-seq) data for transcriptome profiling.
  • Application of complex computational methods for the detection and annotation of known and novel ncRNAs.
  • Compilation of relevant software packages and databases for plant ncRNA discovery.

Main Results:

  • RNA-seq enables a comprehensive view of the non-coding transcriptome.
  • Specific computational approaches are required to identify diverse ncRNA classes from RNA-seq data.
  • A curated bioinformatics toolbox is presented for plant ncRNA researchers.

Conclusions:

  • Accurate identification and annotation of plant ncRNAs are crucial for functional studies.
  • Advanced computational strategies are necessary to overcome challenges in ncRNA detection from RNA-seq.
  • This review provides a foundation for the comprehensive discovery of plant ncRNAs.