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Updated: May 29, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
The evolutionary origin of orphan genes.
Diethard Tautz1, Tomislav Domazet-Lošo
1Max-Planck Institut für Evolutionsbiologie, August-Thienemannstrasse 2, 24306 Plön, Germany. tautz@evolbio.mpg.de
Nature Reviews. Genetics
|September 1, 2011
Summary
New gene evolution arises not only from duplication but also from de novo origins in non-coding DNA. This process continuously provides novel gene functions for lineage-specific adaptations.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Traditional models emphasize gene duplication and rearrangement as primary drivers of evolution.
- Orphan genes, lacking homologs in other lineages, present a challenge to understanding evolutionary origins.
- The evolutionary pathways for orphan genes remain incompletely understood.
Purpose of the Study:
- To explore alternative mechanisms driving gene evolution beyond duplication and rearrangement.
- To investigate the role of de novo gene formation in the emergence of orphan genes.
- To understand how new gene functions arise and contribute to lineage-specific adaptations.
Main Methods:
- Comparative genomics analysis to identify orphan genes across evolutionary lineages.
- Bioinformatic approaches to trace the potential origin of orphan genes from non-coding regions.
- Functional analysis to assess the potential roles of newly evolved genes.
Main Results:
- Evidence suggests de novo evolution from non-coding genomic regions is a significant source of new genes.
- Orphan genes can arise through rapid divergence following duplication or entirely new formation.
- De novo gene birth provides a continuous source of novel genetic material.
Conclusions:
- De novo gene evolution is a crucial, underappreciated mechanism complementing duplication and rearrangement.
- The emergence of orphan genes through de novo pathways fuels evolutionary innovation.
- This mechanism offers raw material for lineage-specific adaptations and functional diversification.
Related Concept Videos
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...
02:32Exon 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...
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.
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.