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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)427-437
Number of pages11
JournalNature Genetics
Volume48
Issue number4
DOIs
StatePublished - Mar 29 2016

ASJC Scopus subject areas

  • Genetics

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    Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A. M., Campbell, M. S., Barrell, D., Martin, K. J., Mulley, J. F., Ravi, V., Lee, A. P., Nakamura, T., Chalopin, D., ... Postlethwait, J. H. (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, 48(4), 427-437. https://doi.org/10.1038/ng.3526