A high fidelity approach to assembling the complex Borrelia genome

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.