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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
JoVE Journal
Genetics
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JoVE Journal Genetics
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

DOI:
10.3791/62872-v

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12:08 min

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August 20, 2021

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, , , , ,
1Department of Biological Sciences,University of Texas at Dallas, 2Department of Urology,University of Texas Southwestern Medical Center

Chapters

  • 00:04Introduction
  • 01:00dsDNA Pool Cleanup and Concentration
  • 03:25Sequence the Genome Library
  • 05:14Long (MinION) Reads
  • 06:55Generating Hybrid Genome Assembly
  • 08:34Assessing Assembly Quality
  • 09:34Genome Annotation
  • 10:07Results: Analysis of Extracted DNA and Complete Genome Sequencing of Urinary Bacteria
  • 11:37Conclusion

Summary

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This protocol details a comprehensive approach for the culturing, sequencing, and de novo hybrid genome assembly of urinary bacteria. It provides a reproducible procedure for the generation of complete, circular genome sequences useful in studying both chromosomal and extrachromosomal genetic elements contributing to urinary colonization, pathogenesis, and antimicrobial resistance dissemination.

Tags

Keywords: Hybrid Genome AssemblyUrinary BacteriaShort-read SequencingLong-read SequencingComplete GenomesGenome ArchitectureMobile Genetic ElementsCulturable BacteriaGenome ContentAdapter LigationFlow Cell PrimingDNA Library PreparationSequencing Run

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