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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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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.
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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
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Related Experiment Video

Updated: Jun 25, 2025

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

Dennis Carhuaricra-Huaman1,2, João Carlos Setubal3

  • 1Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Sao Paulo, SP, Brazil.

Methods in Molecular Biology (Clifton, N.J.)
|May 31, 2024
PubMed
Summary

This study presents a comprehensive bioinformatics workflow for analyzing bacterial genomes. Researchers can use this protocol to explore bacterial diversity, identify key genes, and understand evolutionary relationships using open-source tools.

Keywords:
BacteriaPangenomePhylogenetic analysisComparative genomics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Thousands of bacterial genome sequences are publicly available, offering significant potential for detailed diversity studies.
  • Comparative genomics enables in-depth analysis of bacterial populations and their genetic makeup.

Purpose of the Study:

  • To describe a complete bioinformatics workflow for comparative analysis of bacterial genomes.
  • To provide a practical, step-by-step protocol for researchers with basic bioinformatics expertise.

Main Methods:

  • The workflow encompasses genome annotation, pangenome reconstruction and visualization, and phylogenetic analysis.
  • It utilizes state-of-the-art, open-source tools and is demonstrated using Salmonella enterica serovar Typhimurium.
  • The protocol relies on Linux commands and scripts, with results visualized using the R environment.

Main Results:

  • The workflow facilitates the identification of specific genetic elements, including antimicrobial-resistance genes, virulence factors, and phage sequences.
  • It enables detailed comparative genomic investigations of bacterial datasets.
  • The study provides a reproducible method for bacterial genome analysis.

Conclusions:

  • This bioinformatics workflow empowers researchers to conduct detailed comparative genomic studies of bacteria.
  • The protocol enhances the exploration of bacterial diversity and the identification of functionally relevant genomic features.
  • Accessible, open-source tools make advanced bacterial genomics research more attainable.