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Gene Duplication and Divergence02:37

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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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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.
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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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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Recurrent sequence evolution after independent gene duplication.

Samuel H A von der Dunk1, Berend Snel2

  • 1Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584, CH, The Netherlands. s.h.a.vonderdunk@uu.nl.

BMC Evolutionary Biology
|August 11, 2020
PubMed
Summary

Recurrent sequence evolution in duplicated genes is common in eukaryotes, revealing predictable functional differentiation and patterns of subcellular localization changes. This study highlights specific gene families and offers insights into the biochemical basis of paralog evolution.

Keywords:
Independent gene duplicationPredictabilityRecurrent evolutionRepeated substitutionsSubfunctionalization

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Molecular Evolution

Background:

  • Convergent and parallel evolution offer insights into natural selection mechanisms.
  • Recurrent amino acid substitutions can be adaptive or selectively neutral.
  • While ortholog recurrent evolution is largely explained by neutral processes, paralog evolution after duplication remains less understood.

Purpose of the Study:

  • To develop a framework for detecting recurrent sequence evolution patterns in duplicated genes.
  • To analyze genomes of 90 eukaryotes to identify recurrent sequence differentiation in paralogs.
  • To investigate the extent and nature of predictable functional differentiation following gene duplication.

Main Methods:

  • Development of a computational framework to detect recurrent sequence evolution patterns.
  • Application of the framework to analyze the genomes of 90 diverse eukaryotic species.
  • Analysis of sequence divergence patterns, including asymmetry and subcellular localization changes.

Main Results:

  • A significant number of gene families exhibit predictable functional differentiation after duplication.
  • Over ten independent duplications in some protein families show similar sequence-level differentiation between paralogs.
  • Approximately 6% of recurrent sequence evolution in paralogs is linked to recurrent differentiation in subcellular localization, with specific patterns identified for Hint1/Hint2, Sco1/Sco2, and vma11/vma3.

Conclusions:

  • The developed methodology enables the study of the biochemical basis for functional differentiation between paralogs.
  • Identified recurrent substitutions, such as in Sco1/Sco2 paralogs, allow for direct experimental validation of their biological roles.
  • The study reveals diverse gene families with recurrent sequence evolution, highlighting trends in functional and evolutionary trajectories of this phenomenon.