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

Ingo Braasch 1, 2 Andrew R. Gehrke 3 Jeramiah J. Smith 4 Kazuhiko Kawasaki 5, 6 Tereza Manousaki 7 Jérémy Pasquier 8 Angel Amores 1 Thomas Desvignes 1 Peter Batzel 1 Julian Catchen 9 Aaron M. Berlin 10 Michael S. Campbell 11, 12 Daniel Barrell 13, 14, 15 Kyle J. Martin 16, 17 John F. Mulley 18 Vydianathan Ravi 19 Alison P. Lee 19 Tetsuya Nakamura 3 Domitille Chalopin 20, 21 Shaohua Fan 4, 21 Dustin Wcisel 22, 23 Cristian Cañestro 24, 25 Jason Sydes 1 Felix E.G. Beaudry 4 Yi Sun 26, 27 Jana Hertel 28, 29 Michael J. Beam 1 Mario Fasold 28 Mikio Ishiyama 30 Jeremy Johnson 10 Steffi Kehr 28 Marcia Lara 10 John H. Letaw 1 Gary W. Litman 31 Ronda T. Litman 31 Masato Mikami 32 Tatsuya Ota 33 Nil Ratan Saha 34 Louise Williams 10 Peter F. Stadler 28 Han Wang 26, 27 John S. Taylor 4 Quenton Fontenot 35 Allyse Ferrara 35 Stephen M.J. Searle 13 Bronwen Aken 13, 36 Mark Yandell 11 Igor Schneider 37 Jeffrey A Yoder 38, 39 Jean-Nicolas Volff 20 Axel Meyer 4, 40 Chris T Amemiya 34 Byrappa Venkatesh 19 Peter W.H. Holland 16 Yann Guiguen 8 Julien Bobe 8 Neil H. Shubin 3 Federica Di Palma 10, 41 Jessica Alföldi 10 Kerstin Lindblad-Toh 10, 42 John H. Postlethwait 1
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.
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Ingo Braasch, Andrew R. Gehrke, Jeramiah J. Smith, Kazuhiko Kawasaki, Tereza Manousaki, et al.. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, Nature Publishing Group, 2016, 48 (4), pp.427-437. ⟨10.1038/ng.3526⟩. ⟨hal-01595410⟩

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