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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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.
In contrast, regions which code...
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...
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...
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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Related Experiment Video

Updated: May 26, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Published on: February 3, 2023

Genomic distance under gene substitutions.

Marília D V Braga1, Raphael Machado, Leonardo C Ribeiro

  • 1Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias, 25250-020, Brazil. mdbraga@inmetro.gov.br

BMC Bioinformatics
|December 14, 2011
PubMed
Summary

This study introduces a new model for calculating genomic distance that efficiently handles non-common markers using substitutions. This method offers a more parsimonious genomic distance for genomes without duplicated markers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Traditional genomic distance calculations often focus only on common markers.
  • Existing models for non-common markers treat insertions and deletions at the same position as two separate events.
  • This can inflate the calculated genomic distance, especially in genomes with significant structural variations.

Purpose of the Study:

  • To develop a novel model for computing genomic distance that accounts for non-common markers more accurately.
  • To introduce substitutions as a unified operation for insertions and deletions at the same genomic position.
  • To provide a more parsimonious measure of genomic distance for comparative genomics.

Main Methods:

  • The study proposes a new model that conceptualizes simultaneous insertions and deletions at the same genomic locus as a single substitution event.
  • This model integrates substitutions with double-cut-and-join (DCJ) operations.
  • A linear time algorithm is presented for computing genomic distance under this model.

Main Results:

  • The new model efficiently sorts non-common markers using substitutions, reducing the count for simultaneous insertion-deletion events to a single step.
  • A linear time algorithm is provided for calculating genomic distance, considering both substitutions and DCJ operations.
  • This approach yields a parsimonious genomic distance for genomes lacking duplicated markers.

Conclusions:

  • The proposed model offers a lower bound for genomic distance in practice for genomes free of duplicated markers.
  • This method can refine orthology assignments by identifying potential unannotated orthologs through substitution events.
  • The approach enhances comparative genomics by providing a more accurate distance measure for unequal genomes.