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Updated: Jun 18, 2026

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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Ubiquitous internal gene duplication and intron creation in eukaryotes.
1Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA. gao3@indiana.edu
Summary
Internal gene segment duplications are frequent evolutionary events, contributing to genomic novelty and intron gain. This study highlights their significant role in shaping genomes.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Genomic segment duplications are a key source of evolutionary novelty.
- Previous research primarily focused on complete gene duplications, neglecting internal gene segment duplications.
Purpose of the Study:
- To investigate the frequency and evolutionary significance of internal gene segment duplications.
- To determine the impact of internal duplications on intron acquisition and genomic novelty.
Main Methods:
- Analysis of six fully sequenced genomes.
- Quantification of internal gene segment duplication rates.
- Identification of genes with duplicated intronic and/or exonic regions.
Main Results:
- Internal gene segment duplications occur at a high frequency (0.001-0.013 duplications/gene/million years).
- 8-17% of genes harbor duplicated intronic and/or exonic regions.
- 7-30% of these genes acquired novel introns via duplication or splice site activation.
Conclusions:
- Internal gene duplications play a major role in generating genomic novelties.
- Internal duplications are a significant mechanism for intron gain during evolution.
Related Concept Videos
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.
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.
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...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
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 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.
Organization of Genes
Overview
Gene 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...
