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Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.

Elisavet Iliopoulou1,2, Vasileios Papadogiannis1,3, Costas S Tsigenopoulos1

  • 1Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology & Aquaculture (IMBBC), Heraklion, Greece.

Genome Biology and Evolution
|April 22, 2024
PubMed
Summary

Conserved noncoding elements in teleosts show significant loss early in evolution but also massive gains in the teleost stem-group. These newly gained elements are crucial for development and can aid teleost phylogenetics.

Keywords:
CNEconserved noncoding elementsenhancer evolutionteleost comparative genomicswhole-genome duplication

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Area of Science:

  • Evolutionary genomics
  • Comparative genomics
  • Developmental biology

Background:

  • Conserved noncoding elements (CNEs) are vital regulatory regions in vertebrates, often located near developmental genes.
  • Previous studies indicated CNE loss and rapid divergence in teleosts, but with limited genomic data.

Purpose of the Study:

  • To investigate the evolution of teleost conserved noncoding elements using an expanded set of high-quality teleost genomes.
  • To identify and characterize CNE gain and loss dynamics throughout teleost evolutionary history.
  • To assess the utility of CNEs for teleost phylogenetics.

Main Methods:

  • Targeted genomic alignments and comparisons across the teleost phylogeny.
  • Synteny-based association to link CNEs with their putatively regulated target genes.
  • Analysis of motif and transcription factor binding site vocabulary in teleost CNEs.

Main Results:

  • Confirmed extensive loss of vertebrate CNEs early in teleost evolution.
  • Discovered massive gain of CNEs in the teleost stem-group over 300 million years ago.
  • Identified newly gained teleost CNEs near developmental and transcriptional regulation genes, sharing similar regulatory vocabulary with vertebrate CNEs.
  • Demonstrated the potential of pan-teleost CNEs for accurate phylogenetic placement.

Conclusions:

  • Early teleost CNE evolution involved both significant loss and substantial gain, possibly through divergence and de novo emergence.
  • Newly acquired CNEs play a role in teleost-specific gene regulation, particularly in development.
  • Pan-teleost CNEs represent valuable markers for resolving teleost evolutionary relationships.