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Related Concept Videos

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 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.
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.
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
DNA-only Transposons02:57

DNA-only Transposons

DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...

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DCJ path formulation for genome transformations which include insertions, deletions, and duplications.

Sophia Yancopoulos1, Richard Friedberg

  • 1Feinstein Institute for Medical Research, Chiovazzi Lab, 350 Community Drive, Manhasset, NY 11030, USA. Sopheetsa@aol.com

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|October 7, 2009
PubMed
Summary
This summary is machine-generated.

This study expands genome rearrangement analysis to genomes with varying gene content and copy numbers using generalized double cut and join (DCJ) operations. New methods, including "ghost adjacencies," accurately calculate genomic distances for complex evolutionary events.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Comparative genomics often assumes equal gene content between genomes.
  • Existing genome rearrangement models, like double cut and join (DCJ), are limited when dealing with unequal gene content or multiple gene copies.
  • Unmatched gene ends in comparative genomes complicate the analysis of evolutionary pathways.

Purpose of the Study:

  • To extend the double cut and join (DCJ) paradigm for analyzing genome rearrangements between genomes with unequal gene content and/or multiple gene copies.
  • To introduce novel concepts like 'ghost adjacencies' and 'nughs' to handle unmatched gene ends and complex genomic structures.
  • To develop a generalized method for calculating DCJ distance that accounts for insertions, deletions, and duplications.

Main Methods:

  • Extension of the double cut and join (DCJ) operation to accommodate genomes with unmatched genes.
  • Introduction of 'ghost adjacencies' to represent missing gene ends and close paths in the generalized adjacency graph.
  • Definition of generalized DCJ operations and a prescription for calculating DCJ distance, including insertions, deletions, and duplications.
  • Development of algorithms for optimal graph closure with and without 'nughs' (half ghost, half null).

Main Results:

  • The study successfully extends the DCJ framework to handle genomes with unequal gene content and copy numbers.
  • New types of paths are identified in the adjacency graph due to unmatched gene ends, requiring novel closure mechanisms.
  • A generalized DCJ distance calculation is provided, incorporating insertions, deletions, and duplications.
  • Algorithms for optimal closure and distance formulas based on paths are presented, with specific calculations for simple cases.

Conclusions:

  • The generalized DCJ framework provides a robust method for inferring genome rearrangements in the presence of gene content variation and duplications.
  • 'Ghost adjacencies' and 'nughs' are effective tools for managing unmatched gene ends and calculating evolutionary distances accurately.
  • This work expands the toolkit for comparative genomics, enabling more precise evolutionary analyses of diverse genomes.