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Related Experiment Video

Updated: Jul 23, 2025

Cultivation Methods of Spirochetes from Borrelia burgdorferi Sensu Lato Complex and Relapsing Fever Borrelia
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A high fidelity approach to assembling the complex Borrelia genome.

Sabrina Hepner1,2, Konstantin Kuleshov3, Ave Tooming-Kunderud4

  • 1German National Reference Centre for Borrelia, Oberschleissheim, Germany. sabrina.hepner@lgl.bayern.de.

BMC Genomics
|July 17, 2023
PubMed
Summary

This study presents a new workflow using high-fidelity sequencing to achieve complete Borrelia burgdorferi genome assemblies, including complex plasmids. This advances understanding of Lyme borreliosis genetics.

Keywords:
Borrelia burgdorferiDe novo assemblyGenome reconstruction pipelineGenomicsHiFi sequencingPlasmids

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Area of Science:

  • Genomics
  • Microbiology
  • Bioinformatics

Background:

  • Borrelia burgdorferi sensu lato (s.l.) causes Lyme borreliosis, but genetic adaptations remain unclear due to incomplete genome data.
  • Assembling complex Borrelia genomes with numerous dynamic plasmids is challenging, even with advanced sequencing methods.

Purpose of the Study:

  • To develop and optimize a workflow for generating complete, high-quality Borrelia genome assemblies.
  • To overcome challenges in reconstructing complex bacterial genomes, particularly plasmids.

Main Methods:

  • Utilized high-fidelity (HiFi) PacBio sequencing technology.
  • Developed and applied a de novo genome assembly workflow incorporating multiple assemblers and refinement steps.
  • Critically appraised existing techniques for genome assembly and quality control.

Main Results:

  • Demonstrated that a combination of HiFi data and an ensemble reconstruction pipeline can fully resolve complex Borrelia genomes.
  • Successfully achieved gap-free reconstruction of both chromosomal and plasmid sequences.
  • Showcased the insufficiency of stand-alone sequencing and assembly methods for complete Borrelia genomes.

Conclusions:

  • The developed pipeline enables complete resolution of chromosomal and plasmid sequences for complex genomes like Borrelia.
  • This approach, using HiFi data and ensemble reconstruction, offers a robust method for Borrelia genome assembly.
  • The pipeline has potential applications for assembling other complex microbial genomes.