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Exon Recombination02:32

Exon Recombination

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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...
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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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...
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Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Cancer-Critical Genes II: Tumor Suppressor Genes01:05

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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
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Related Experiment Video

Updated: Jan 7, 2026

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia
05:51

A Strategy to Identify de Novo Mutations in Common Disorders such as Autism and Schizophrenia

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Candidate orphan genes: Reassessing uniqueness.

Sheetalpreet K Maan1,2,3,4, Xuan Y Butzin1,2,3,4, Steven X Ge2,5

  • 1Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America.

Plos One
|December 31, 2025
PubMed
Summary
This summary is machine-generated.

The prevalence of orphan genes in bacteria has been overestimated due to limited genomic data. Reanalysis shows an 81% decrease, suggesting many are not truly unique and should be labeled as 'candidate' or 'putative' genes.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Related Experiment Videos

Last Updated: Jan 7, 2026

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Orphan genes lack homologs outside a taxonomic unit, posing challenges to evolutionary models.
  • They are implicated in lineage-specific traits, virulence, and adaptation.
  • Previous estimates of orphan gene prevalence may be inflated due to limited data.

Purpose of the Study:

  • To re-evaluate the prevalence of orphan genes in bacteria using an updated dataset.
  • To reassess the evolutionary origins and taxonomic distribution of previously identified orphan genes.
  • To propose revised annotation standards for genes with apparent uniqueness.

Main Methods:

  • Analysis of a comprehensive 2023 dataset of bacterial genes from over 80,000 species.
  • Homology-based analyses to determine gene distribution across broader genomic landscapes.
  • Application of computational filters to identify high-confidence candidate proteins.

Main Results:

  • Reassessment revealed an 81% decrease in the number of orphan genes within two years.
  • Many previously classified orphan genes were found to have homologs in other bacterial taxa.
  • The study identified a refined, high-confidence subset of candidate genes for further validation.

Conclusions:

  • The prevalence of bacterial orphan genes has been significantly overestimated.
  • Orphan genes should be annotated as 'candidate' or 'putative' to reflect their provisional status.
  • This study provides a refined dataset and annotation recommendations for future research.