Skip to main content
eScholarship
Open Access Publications from the University of California

UC Merced

UC Merced Previously Published Works bannerUC Merced

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

  • Author(s): Braasch, Ingo
  • Gehrke, Andrew R
  • Smith, Jeramiah J
  • Kawasaki, Kazuhiko
  • Manousaki, Tereza
  • Pasquier, Jeremy
  • Amores, Angel
  • Desvignes, Thomas
  • Batzel, Peter
  • Catchen, Julian
  • Berlin, Aaron M
  • Campbell, Michael S
  • Barrell, Daniel
  • Martin, Kyle J
  • Mulley, John F
  • Ravi, Vydianathan
  • Lee, Alison P
  • Nakamura, Tetsuya
  • Chalopin, Domitille
  • Fan, Shaohua
  • Wcisel, Dustin
  • Cañestro, Cristian
  • Sydes, Jason
  • Beaudry, Felix EG
  • Sun, Yi
  • Hertel, Jana
  • Beam, Michael J
  • Fasold, Mario
  • Ishiyama, Mikio
  • Johnson, Jeremy
  • Kehr, Steffi
  • Lara, Marcia
  • Letaw, John H
  • Litman, Gary W
  • Litman, Ronda T
  • Mikami, Masato
  • Ota, Tatsuya
  • Saha, Nil Ratan
  • Williams, Louise
  • Stadler, Peter F
  • Wang, Han
  • Taylor, John S
  • Fontenot, Quenton
  • Ferrara, Allyse
  • Searle, Stephen MJ
  • Aken, Bronwen
  • Yandell, Mark
  • Schneider, Igor
  • Yoder, Jeffrey A
  • Volff, Jean-Nicolas
  • Meyer, Axel
  • Amemiya, Chris T
  • Venkatesh, Byrappa
  • Holland, Peter WH
  • Guiguen, Yann
  • Bobe, Julien
  • Shubin, Neil H
  • Di Palma, Federica
  • Alföldi, Jessica
  • Lindblad-Toh, Kerstin
  • Postlethwait, John H
  • et al.

Published Web Location

https://doi.org/10.1038/ng.3526
Abstract

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Main Content
Current View