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Related Experiment Videos

Visualization of consensus genome structure without using a reference genome.

Ipputa Tada1,2, Yasuhiro Tanizawa1, Masanori Arita3,4

  • 1Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.

BMC Genomics
|April 1, 2017
PubMed
Summary
This summary is machine-generated.

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A new circular genome visualizer enables reference-free whole genome comparison by mapping orthologous gene clusters. This method reveals large-scale rearrangements and strain-specific genomic islands in bacterial species.

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative genomics

Background:

  • Whole genome comparison typically relies on a reference genome, which can introduce biases and limitations.
  • Existing methods are insufficient for the vast amount of sequence data from new sequencing technologies.
  • There is a need for reference-free genome comparison methods.

Purpose of the Study:

  • To develop a novel tool for comparing complete genomes of closely related species without a reference genome.
  • To visualize orthologous gene cluster positions for comparative analysis.
  • To identify genomic rearrangements and strain-specific regions.

Main Methods:

  • Introduction of a circular genome visualizer.
  • Visualization of orthologous gene cluster positions, not sequences.
Keywords:
Circular visualizationComparative genomicsHelicobacter pyloriLactobacillus casei

Related Experiment Videos

  • Color-coding of gene cluster positions in circular graphics.
  • Application to Lactobacillus paracasei and Helicobacter pylori strains.

    • Main Results:

    • The tool successfully compares genomes without a reference.
    • Analysis of Lactobacillus paracasei strains revealed large-scale rearrangements and strain-specific genomic islands.
    • Comparison of Helicobacter pylori strains showed genetic consistency and identified three patterns of genome inversions.

    Conclusions:

    • Reference-free genome comparison is feasible using orthologous gene cluster positions.
    • The method allows identification of conserved and strain-specific genomic regions.
    • Positional comparison aids in detecting large-scale genome rearrangements and gene transfers.