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Related Concept Videos

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.
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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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.
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Related Experiment Video

Updated: Nov 8, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation
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Evolution after Whole-Genome Duplication: Teleost MicroRNAs.

Thomas Desvignes1, Jason Sydes1, Jerôme Montfort2

  • 1Institute of Neuroscience, University of Oregon, Eugene, OR, USA.

Molecular Biology and Evolution
|April 19, 2021
PubMed
Summary

Following whole-genome duplication, microRNA (miRNA) genes were retained more than protein-coding genes, influencing developmental canalization and phenotypic diversification. This study reveals key mechanisms of miRNA evolution in metazoans after gene duplication events.

Keywords:
Japanese medaka Oryzias latipesarm-switchingblackfin icefish Chaenocephalus aceratusspotted gar Lepisosteus oculatusthree-spined stickleback Gasterosteus aculeatuszebrafish Danio rerio

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular biology

Background:

  • MicroRNAs (miRNAs) regulate gene expression and are crucial for biological processes.
  • The evolution of miRNA genes and their role in developmental canalization and phenotypic diversification remain incompletely understood.
  • Whole-genome duplication (WGD) events can drive species divergence and phenotypic change by increasing gene numbers.

Purpose of the Study:

  • To investigate the evolutionary consequences of genome duplication on miRNA gene evolution.
  • To analyze miRNA gene retention, loss, and expression patterns after the teleost genome duplication (TGD).
  • To understand the impact of genomic context and strand bias on miRNA evolution.

Main Methods:

  • Comparative genomics analysis of miRNA genes in four teleost species and spotted gar.
  • Analysis of miRNA gene retention rates in ohnologous pairs compared to protein-coding genes.
  • Examination of miRNA gene expression patterns and evolutionary pressures on different miRNA strands.

Main Results:

  • miRNA genes were retained more frequently than protein-coding genes following the TGD, with rapid gene loss observed.
  • Genomic context significantly influenced retention rates; clustered and intergenic miRNAs showed higher retention.
  • Expression analyses revealed conserved and divergent patterns, suggesting roles in both canalization and diversification. Major miRNA strands experienced stronger purifying selection, particularly in seed regions.

Conclusions:

  • WGD events significantly shape miRNA gene evolution, influencing gene retention and loss dynamics.
  • Genomic location and strand bias are critical factors in miRNA evolution post-duplication.
  • The study provides a comprehensive, genome-wide perspective on metazoan miRNA evolution following WGD, highlighting their roles in phenotypic evolution.