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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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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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...
14.3K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.0K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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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...
175
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

6.6K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.6K
Synteny and Evolution02:31

Synteny and Evolution

3.4K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.4K

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Related Experiment Video

Updated: Sep 23, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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plotsr: visualizing structural similarities and rearrangements between multiple genomes.

Manish Goel1,2, Korbinian Schneeberger1,2

  • 1Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany.

Bioinformatics (Oxford, England)
|May 13, 2022
PubMed
Summary

New genome sequencing tools enable detailed comparison of multiple species genomes. Plotsr visualizes structural similarities and rearrangements, aiding genomic research and discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Advancements in third-generation sequencing have increased the availability of high-quality genome assemblies.
  • Comparing multiple genome assemblies necessitates novel tools for visualizing structural properties.

Purpose of the Study:

  • To introduce plotsr, an efficient software tool for visualizing structural similarities and rearrangements between genomes.
  • To provide a flexible platform for chromosome-level genome comparisons and detailed regional analysis.

Main Methods:

  • plotsr is implemented as a Python package utilizing the matplotlib library.
  • The tool supports visualization of structural variations and rearrangements at various scales.
  • Augmentation of visualizations with regional identifiers (genes, markers) and continuous feature histograms (GC content, polymorphism density) is supported.

Main Results:

  • plotsr enables efficient visualization of structural genome properties.
  • The tool facilitates detailed comparisons of genome structures, from chromosome level to specific regions.
  • Customizable visualizations can incorporate genomic features and continuous data tracks.

Conclusions:

  • plotsr is a valuable new tool for comparative genomics.
  • The software enhances the ability to analyze and interpret structural variations in newly assembled genomes.
  • plotsr is freely available, promoting its adoption in the research community.