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Updated: May 24, 2026
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Analysis of gene order evolution beyond single-copy genes.
Nadia El-Mabrouk1, David Sankoff
1Département d'Informatique et de Recherche Opérationnelle, Université de Montréal, Montréal, QC, Canada.
Methods in Molecular Biology (Clifton, N.J.)
|March 13, 2012
Summary
This chapter reviews genome rearrangement and comparative genomics, focusing on handling duplicated genes to understand genome evolution and ancestral structures. It explores gene order, duplication, and rearrangement events across different biological scales.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Comparative genomics analyzes genome evolution by representing genomes as ordered sequences of genes.
- Understanding gene order and duplications is crucial for reconstructing evolutionary histories.
Purpose of the Study:
- To provide a comprehensive review of genome rearrangement, emphasizing the challenge of duplicated genes.
- To explore realistic evolutionary scenarios for gene order changes and ancestral genome content.
Main Methods:
- Reviewing methods for representing genomes as ordered sequences of genes or blocks.
- Addressing challenges in orthology, paralogy, and synteny block identification.
- Examining gene organization at gene family, cluster, and genome levels.
Main Results:
- The study outlines approaches to identify gene orthology, paralogy, and synteny blocks.
- It details evolutionary processes including duplication, loss, speciation, tandem duplications, and whole genome duplications.
- The review synthesizes current understanding of genome rearrangement mechanisms.
Conclusions:
- Accurate genome representation is fundamental for studying genome evolution.
- Handling duplicated genes is a key challenge in comparative genomics.
- A multi-level approach is necessary to understand complex genome rearrangement events.
Related Concept Videos
02:37Gene 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.
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.
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
02:05Gene 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...
In contrast, regions which code...
02:05Gene 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...
In contrast, regions which code...
03:21Genome 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.