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Identification of Circular RNAs using RNA Sequencing
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Full-Length Sequencing of Circular DNA Viruses Using CIDER-Seq.

Syed Shan-E-Ali Zaidi1,2, Victor Golyaev3,4, Devang Mehta4,5

  • 1Plant Genetics Lab, TERRA Research and Teaching Centre, Gembloux Agro BioTech, University of Liège, Gembloux, Belgium.

Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2025
PubMed
Summary

Circular DNA Enrichment Sequencing (CIDER-Seq) enables full-length viral genome sequencing for virus discovery and population analysis. This method combines PCR-free enrichment with long-read sequencing and a de-concatenation algorithm for accurate circular DNA virus genomes.

Keywords:
CIDER-SeqCircular DNAGeminivirusLong-read sequencingOxford nanoporePacBio

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Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Full-length viral genome sequencing is crucial for understanding virus distribution, discovering novel viruses, and analyzing viral populations.
  • Circular DNA viruses present unique sequencing challenges due to their genome structure.

Purpose of the Study:

  • To introduce and validate Circular DNA Enrichment Sequencing (CIDER-Seq) for unbiased enrichment and long-read sequencing of circular DNA viruses.
  • To develop a computational pipeline for assembling complete circular viral genomes from sequencing data.

Main Methods:

  • CIDER-Seq employs PCR-free enrichment coupled with Single Molecule Real-Time (SMRT) sequencing.
  • The DeConcat algorithm is utilized to process SMRT sequencing data and reconstruct intact circular DNA sequences.

Main Results:

  • CIDER-Seq successfully generates single-read, full-length viral genomes.
  • The DeConcat algorithm effectively de-concatenates sequencing reads into complete circular DNA virus genomes.
  • The method produces fully annotated and highly accurate circular DNA virus genome sequences.

Conclusions:

  • CIDER-Seq provides a robust and unbiased method for sequencing circular DNA viruses.
  • This approach facilitates comprehensive viral genome analysis, aiding in discovery and population studies.
  • The integrated data analysis package ensures high accuracy in reconstructing viral genomes.