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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 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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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Updated: Jun 22, 2025

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
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Published on: November 12, 2012

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zDB: bacterial comparative genomics made easy.

Bastian Marquis1, Trestan Pillonel1, Alessia Carrara1

  • 1Lausanne University Hospital and University of Lausanne, Institute of Microbiology, Lausanne, Switzerland.

Msystems
|June 28, 2024
PubMed
Summary
This summary is machine-generated.

zDB is a new application that integrates genomic analysis and visualization tools, simplifying comparative genomics for researchers. It automates complex tasks and provides an intuitive platform for exploring genomic data and evolutionary relationships.

Keywords:
comparative genomicsgenome visualizationmicrobial genomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome analysis and comparison require diverse, specialized tools.
  • Integrating results from multiple tools is a significant challenge for researchers.
  • A unified platform for genomic analysis and visualization is needed.

Purpose of the Study:

  • To develop zDB, an integrated application for comparative genomics.
  • To streamline genome analysis, orthology prediction, and phylogenetic inference.
  • To provide an intuitive visualization platform for exploring genomic data.

Main Methods:

  • Developed zDB with a Nextflow analysis pipeline and a Python/Django visualization platform.
  • Automated gene annotation, orthology prediction, and phylogenetic tree construction.
  • Integrated Pfam, COG, KEGG, and Swissprot annotations for enriched analysis.

Main Results:

  • zDB identifies orthologs, infers gene and species phylogenies.
  • The platform allows searching genes, running BLAST, and comparing genomic regions/genomes.
  • Users can visualize metabolic capacities and gene conservation using various formats (Venn diagrams, heatmaps).

Conclusions:

  • zDB simplifies complex comparative genomic analyses.
  • The tool supports both bioinformaticians and laboratory researchers.
  • zDB facilitates data sharing and exploratory analysis across diverse genomic datasets.