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Time-lapse imaging of molecular evolution by high-throughput sequencing.

Nam Nguyen Quang1,2,3, Clément Bouvier1,2,4, Adrien Henriques1,2,3

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High-throughput sequencing (HTS) reconstructs empirical evolutionary trees for aptamers, revealing molecular evolution dynamics. This method tracks sequence proliferation and extinction, offering insights into fitness and evolutionary pathways during selection.

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Area of Science:

  • Molecular Evolution
  • Biotechnology
  • Bioinformatics

Background:

  • In vitro selection generates large datasets of molecular sequences.
  • Understanding molecular evolution pathways requires tracking sequence changes over time.
  • Classical phylogenetic trees do not capture population dynamics during selection.

Purpose of the Study:

  • To demonstrate the use of high-throughput sequencing (HTS) for reconstructing empirical genealogical evolutionary (EGE) trees.
  • To visualize sequence proliferation and extinction dynamics during in vitro selection.
  • To infer evolutionary fitness and mutation pathways of macromolecules.

Main Methods:

  • Application of HTS to analyze sequence populations from in vitro selection experiments.
  • Construction of EGE trees representing sequence evolution and fitness.
  • Re-analysis of a known aptamer selection against Annexin A2.

Main Results:

  • Successfully reconstructed an EGE tree for an aptamer family, illustrating population dynamics.
  • Identified potential ancestral sequences and inferred evolutionary trajectories.
  • Predicted improved aptamer variants and elucidated the impact of selection pressure.

Conclusions:

  • HTS enables the creation of EGE trees, providing a time-lapse view of molecular evolution during in vitro selection.
  • This approach enhances understanding of sequence fitness, mutation, and adaptation.
  • The method offers a powerful tool for aptamer discovery and optimization.