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Updated: May 18, 2026
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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.
Yun Zhu1, Peng Du, Luay Nakhleh
1Department of Computer Science, Rice University, Houston, Texas, United States of America. yun.zhu@rice.edu
Plos One
|September 18, 2012
Summary
Gene duplication drives evolution, influencing gene networks and complexity. This study reveals a growing link between gene duplicability and connectivity across species, while duplicability and complexity remain stable, suggesting neutral evolutionary forces at play.
Area of Science:
- Evolutionary biology
- Genomics
- Bioinformatics
Background:
- Gene duplication is a key evolutionary mechanism shaping genomes.
- Previous studies explored gene duplicability correlations with network connectivity and complexity in limited species.
- Understanding factors influencing gene duplicability is crucial for evolutionary studies.
Purpose of the Study:
- To investigate the correlation between gene duplicability and network connectivity across six diverse species.
- To examine the relationship between gene duplicability and gene complexity across these species.
- To explore the role of neutral evolutionary forces in shaping gene duplicability patterns.
Main Methods:
- Comparative genomic analysis across six species.
- Analysis of gene duplicability, protein-protein interaction network connectivity, and gene complexity.
- Computational simulations to model evolutionary trends.
Main Results:
- A positive correlation between gene duplicability and network connectivity was observed, increasing with genome size and phylogenetic relatedness.
- The correlation between gene duplicability and gene complexity remained consistent across all studied species.
- Simulations supported neutral evolutionary forces as an explanation for the observed duplicability-connectivity trend.
Conclusions:
- Gene duplicability is influenced by genome size and evolutionary history, particularly concerning network interactions.
- Gene complexity appears to be a more conserved factor in relation to gene duplication.
- Neutral evolutionary processes likely play a significant role in shaping gene duplicability, warranting further investigation into both adaptive and non-adaptive factors.
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...
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.
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.
02:08Gene 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...
02:08Gene 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...