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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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 characterized.
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
Exon Recombination02:32

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...

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Related Experiment Video

Updated: Jun 16, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
14:26

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Genome rearrangements with duplications.

Martin Bader1

  • 1Institute of Theoretical Computer Science, Ulm University, 89069 Ulm, Germany. martin.bader@uni-ulm.de

BMC Bioinformatics
|February 4, 2010
PubMed
Summary

This study presents a new algorithm for genome rearrangement that handles gene duplications and deletions in multichromosomal genomes. The method efficiently sorts ancestral genomes into descendant genomes, approaching the true evolutionary distance.

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Comparative genomics often simplifies genomes by assuming single gene copies, which is biologically unrealistic.
  • Real genomes contain duplicated gene content, posing challenges for existing genome rearrangement algorithms.
  • Handling unequal gene content, especially with arbitrary-sized duplications and deletions, remains a significant computational hurdle.

Purpose of the Study:

  • To extend a heuristic algorithm for genome sorting to accommodate multichromosomal genomes.
  • To enable the analysis of genome evolution involving tandem duplications and deletions of arbitrary segment sizes.
  • To develop a computational tool for reconstructing evolutionary histories with complex genomic changes.

Main Methods:

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Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae
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Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae

Published on: September 23, 2011

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Quantitation and Analysis of the Formation of HO-Endonuclease Stimulated Chromosomal Translocations by Single-Strand Annealing in Saccharomyces cerevisiae
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  • Extension of a previously developed heuristic algorithm for genome sorting.
  • Adaptation of the algorithm to handle multichromosomal genomes.
  • Incorporation of operations including reversals, block interchanges, tandem duplications, and deletions of arbitrary size.

    • Main Results:

    • The algorithm successfully sorts multichromosomal genomes.
    • It accommodates a wide range of evolutionary operations, including tandem duplications and deletions.
    • The approach addresses the challenge of unequal gene content in comparative genomics.

    Conclusions:

    • The developed algorithm effectively reconstructs evolutionary pathways for multichromosomal genomes.
    • It provides sorting sequences with evolutionary distances close to the true biological values.
    • This work advances the field of comparative genomics by providing a more realistic model of genome evolution.