Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

60
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
60
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.9K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.9K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.0K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The β-lactam adjuvant guanosine potentiates anti-folate antibiotics and pyrimidine synthesis inhibitors by depleting thymidine in methicillin-resistant <i>Staphylococcus aureus</i>.

Antimicrobial agents and chemotherapy·2026
Same author

The β-lactam adjuvant guanosine potentiates anti-folate antibiotics and pyrimidine synthesis inhibitors by depleting thymidine in methicillin-resistant <i>Staphylococcus aureus</i>.

bioRxiv : the preprint server for biology·2026
Same author

Mutation of lipoprotein processing pathway gene <i>lspA</i> or inhibition of LspA activity by globomycin increases MRSA resistance to β-lactam antibiotics.

Antimicrobial agents and chemotherapy·2025
Same author

A S<sub>180</sub>F substitution in D-alanine aminotransferase confers resistance to β-chloro-D-alanine in Staphylococcus aureus.

The Journal of biological chemistry·2025
Same author

A D-alanine aminotransferase S<sub>180</sub>F substitution confers resistance to β-chloro-D-alanine in <i>Staphylococcus aureus</i> via antibiotic inactivation.

bioRxiv : the preprint server for biology·2025
Same author

Carbene formation as a mechanism for efficient intracellular uptake of cationic antimicrobial carbon acid polymers.

Nature communications·2025

Related Experiment Video

Updated: Aug 1, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

Published on: August 20, 2021

5.1K

Bacterial Whole-Genome-Resequencing Analysis: Basic Steps Using the CLC Genomics Workbench Software.

Merve S Zeden1, Angelika Gründling2

  • 1Microbiology, School of Biological and Chemical Sciences, National University of Galway, Galway H91 TK33, Ireland.

Cold Spring Harbor Protocols
|April 28, 2023
PubMed
Summary

This protocol details bacterial genome resequencing using QIAGEN CLC Genomics Workbench. It demonstrates generating a reference genome and identifying mutations in bacterial strains like Staphylococcus aureus.

More Related Videos

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.3K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.2K

Related Experiment Videos

Last Updated: Aug 1, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
12:08

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

Published on: August 20, 2021

5.1K
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
09:06

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

10.3K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.2K

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Bacterial genome resequencing is crucial for understanding microbial evolution and adaptation.
  • Identifying genomic alterations in mutant strains aids in discovering novel traits and mechanisms.
  • QIAGEN CLC Genomics Workbench offers a comprehensive platform for complex genomic analyses.

Purpose of the Study:

  • To provide a protocol for bacterial genome resequencing analysis using QIAGEN CLC Genomics Workbench.
  • To demonstrate the generation of a reference genome from raw sequencing reads.
  • To illustrate the identification of genomic mutations in bacterial mutant strains.

Main Methods:

  • Utilizing QIAGEN CLC Genomics Workbench for sequence assembly and analysis.
  • Generating a consensus reference genome from Illumina sequencing reads of a wild-type Staphylococcus aureus strain (RN4220).
  • Resequencing a mutant Staphylococcus aureus strain (RN4220 OxaR) and comparing it to the generated reference genome to identify mutations.

Main Results:

  • Successful generation of a consensus reference genome for Staphylococcus aureus RN4220.
  • Identification of specific genomic alterations in the oxacillin-resistant (OxaR) mutant strain.
  • The protocol effectively highlights differences between wild-type and mutant bacterial genomes.

Conclusions:

  • The described protocol provides a robust method for bacterial genome resequencing and mutation detection.
  • QIAGEN CLC Genomics Workbench is a suitable tool for generating reference genomes and analyzing genomic variations.
  • This approach facilitates the study of bacterial adaptation, such as antibiotic resistance development in Staphylococcus aureus.