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Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution.

Marie Kristin Lebherz1, Bharat Ravi Iyengar1, Erich Bornberg-Bauer1,2

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Summary
This summary is machine-generated.

Newly identified de novo genes typically maintain their open reading frame (ORF) length over short evolutionary periods. Significant changes are more likely to result in truncation, though selection may drive elongation over longer timescales.

Keywords:
de novo gene emergencegene evolutiongenomicsmathematical modelingprotein evolution

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Molecular biology

Background:

  • De novo genes arise from previously non-genic DNA, requiring an open reading frame (ORF) and transcription.
  • The length of de novo gene ORFs can change over evolutionary time.
  • Previous studies suggest older de novo genes have longer ORFs, but the mechanism of length change is unclear.

Purpose of the Study:

  • To investigate the evolutionary dynamics of de novo gene open reading frame (ORF) length.
  • To determine if de novo gene ORFs elongate or truncate over evolutionary time.

Main Methods:

  • Developed a mathematical model of ORF elongation as a Markov-jump process.
  • Analyzed genomics and transcriptomics data from seven Drosophila melanogaster populations.

Main Results:

  • The mathematical model predicts that ORFs tend to maintain their length over short evolutionary timescales.
  • The model also indicates that truncations are more probable than elongations when length changes occur.
  • Genomic and transcriptomic data analyses supported the model's predictions.

Conclusions:

  • De novo gene ORF length is generally stable in the short term, with truncations being more common than elongations.
  • Natural selection may drive ORF length extension over longer evolutionary periods, potentially explaining longer ORFs in older de novo genes.
  • Shorter ORFs might be selected against due to a reduced likelihood of producing functional proteins.